Mitochondrial complex I deficiency stratifies idiopathic Parkinson's disease.

Idiopathic Parkinson's disease (iPD) is believed to have a heterogeneous pathophysiology, but molecular disease subtypes have not been identified. Here, we show that iPD can be stratified according to the severity of neuronal respiratory complex I (CI) deficiency, and identify two emerging disease subtypes with distinct molecular and clinical profiles. The CI deficient (CI-PD) subtype accounts for approximately a fourth of all cases, and is characterized by anatomically widespread neuronal CI deficiency, a distinct cell type-specific gene expression profile, increased load of neuronal mtDNA deletions, and a predilection for non-tremor dominant motor phenotypes. In contrast, the non-CI deficient (nCI-PD) subtype exhibits no evidence of mitochondrial impairment outside the dopaminergic substantia nigra and has a predilection for a tremor dominant phenotype. These findings constitute a step towards resolving the biological heterogeneity of iPD with implications for both mechanistic understanding and treatment strategies.

The STRAT-PARK cohort: A personalized initiative to stratify Parkinson's disease.

The STRAT-PARK initiative aims to provide a platform for stratifying Parkinson's disease (PD) into biological subtypes, using a bottom-up, multidisciplinary biomarker-based and data-driven approach. PD is a heterogeneous entity, exhibiting high interindividual clinicopathological variability. This diversity suggests that PD may encompass multiple distinct biological entities, each driven by different molecular mechanisms. Molecular stratification and identification of disease subtypes is therefore a key priority for understanding and treating PD. STRAT-PARK is a multi-center longitudinal cohort aiming to recruit a total of 2000 individuals with PD and neurologically healthy controls from Norway and Canada, for the purpose of identifying molecular disease subtypes. Clinical assessment is performed annually, whereas biosampling, imaging, and digital and neurophysiological phenotyping occur every second year. The unique feature of STRAT-PARK is the diversity of collected biological material, including muscle biopsies and platelets, tissues particularly useful for mitochondrial biomarker research. Recruitment rate is ∼150 participants per year. By March 2023, 252 participants were included, comprising 204 cases and 48 controls. STRAT-PARK is a powerful stratification initiative anticipated to become a global research resource, contributing to personalized care in PD.

Microarchitected Compliant Scaffolds of Pyrolytic Carbon for 3D Muscle Cell Growth.

The integration of additive manufacturing technologies with the pyrolysis of polymeric precursors enables the design-controlled fabrication of architected 3D pyrolytic carbon (PyC) structures with complex architectural details. Despite great promise, their use in cellular interaction remains unexplored. This study pioneers the utilization of microarchitected 3D PyC structures as biocompatible scaffolds for the colonization of muscle cells in a 3D environment. PyC scaffolds are fabricated using micro-stereolithography, followed by pyrolysis. Furthermore, an innovative design strategy using revolute joints is employed to obtain novel, compliant structures of architected PyC. The pyrolysis process results in a pyrolysis temperature- and design-geometry-dependent shrinkage of up to 73%, enabling the geometrical features of microarchitected compatible with skeletal muscle cells. The stiffness of architected PyC varies with the pyrolysis temperature, with the highest value of 29.57 ± 0.78 GPa for 900 °C. The PyC scaffolds exhibit excellent biocompatibility and yield 3D cell colonization while culturing skeletal muscle C2C12 cells. They further induce good actin fiber alignment along the compliant PyC construction. However, no conclusive myogenic differentiation is observed here. Nevertheless, these results are highly promising for architected PyC scaffolds as multifunctional tissue implants and encourage more investigations in employing compliant architected PyC structures for high-performance tissue engineering applications.

NR-SAFE: a randomized, double-blind safety trial of high dose nicotinamide riboside in Parkinson's disease.

Nicotinamide adenine dinucleotide (NAD) replenishment therapy using nicotinamide riboside (NR) shows promise for Parkinson's disease (PD) and other neurodegenerative disorders. However, the optimal dose of NR remains unknown, and doses exceeding 2000 mg daily have not been tested in humans. To evaluate the safety of high-dose NR therapy, we conducted a single-center, randomized, placebo-controlled, double-blind, phase I trial on 20 individuals with PD, randomized 1:1 on NR 1500 mg twice daily (n = 10) or placebo (n = 10) for four weeks. The trial was conducted at the Department of Neurology, Haukeland University Hospital, Bergen, Norway. The primary outcome was safety, defined as the frequency of moderate and severe adverse events. Secondary outcomes were tolerability defined as frequency of mild adverse events, change in the whole blood and urine NAD metabolome, and change in the clinical severity of PD, measured by MDS-UPDRS. All 20 participants completed the trial. The trial met all prespecified outcomes. NR therapy was well tolerated with no moderate or severe adverse events, and no significant difference in mild adverse events. NR therapy was associated with clinical improvement of total MDS-UPDRS scores. However, this change was also associated with a shorter interval since the last levodopa dose. NR greatly augmented the blood NAD metabolome with up to 5-fold increase in blood NAD+ levels. While NR-recipients exhibited a slight initial rise in serum homocysteine levels, the integrity of the methyl donor pool remained intact. Our results support extending the dose range of NR in phase II clinical trials to 3000 mg per day, with appropriate safety monitoring. Clinicaltrials.gov identifier: NCT05344404.

Hexagonal Hybrid Bismuthene by Molecular Interface Engineering.

High-quality devices based on layered heterostructures are typically built from materials obtained by complex solid-state physical approaches or laborious mechanical exfoliation and transfer. Meanwhile, wet-chemically synthesized materials commonly suffer from surface residuals and intrinsic defects. Here, we synthesize using an unprecedented colloidal photocatalyzed, one-pot redox reaction a few-layers bismuth hybrid of "electronic grade" structural quality. Intriguingly, the material presents a sulfur-alkyl-functionalized reconstructed surface that prevents it from oxidation and leads to a tuned electronic structure that results from the altered arrangement of the surface. The metallic behavior of the hybrid is supported by ab initio predictions and room temperature transport measurements of individual nanoflakes. Our findings indicate how surface reconstructions in two-dimensional (2D) systems can promote unexpected properties that can pave the way to new functionalities and devices. Moreover, this scalable synthetic process opens new avenues for applications in plasmonics or electronic (and spintronic) device fabrication. Beyond electronics, this 2D hybrid material may be of interest in organic catalysis, biomedicine, or energy storage and conversion.

Nicotinamide riboside supplementation is not associated with altered methylation homeostasis in Parkinson's disease.

Replenishing nicotinamide adenine dinucleotide (NAD) via supplementation of nicotinamide riboside (NR) has been shown to confer neuroprotective effects in models of aging and neurodegenerative diseases, including Parkinson's disease (PD). Although generally considered safe, concerns have been raised that NR supplementation could impact methylation dependent reactions, including DNA methylation, because of increased production and methylation dependent breakdown of nicotinamide (NAM). We investigated the effect of NR supplementation on DNA methylation in a double blinded, placebo-controlled trial of 29 human subjects with PD, in blood cells and muscle tissue. Our results show that NR had no impact on DNA methylation homeostasis, including individuals with common pathogenic mutations in the MTHFR gene known to affect one-carbon metabolism. Pathway and methylation variance analyses indicate that there might be minor regulatory responses to NR. We conclude that short-term therapy with high-dose NR for up to 30 days has no deleterious impact on methylation homeostasis.

Electrospun carbon nanofibre-assisted patterning of metal oxide nanostructures.

This work establishes carbon nanofibre-mediated patterning of metal oxide nanostructures, through the combination of electrospinning and vapor-phase transport growth. Electrospinning of a suitable precursor with subsequent carbonization results in the patterning of catalyst gold nanoparticles embedded within carbon nanofibres. During vapor-phase transport growth, these nanofibres allow preferential growth of one-dimensional metal oxide nanostructures, which grow radially outward from the nanofibril axis, yielding a hairy caterpillar-like morphology. The synthesis of metal oxide caterpillars is demonstrated using zinc oxide, indium oxide, and tin oxide. Source and substrate temperatures play the most crucial role in determining the morphology of the metal oxide caterpillars, whereas the distribution of the nanofibres also has a significant impact on the overall morphology. Introducing the current methodology with near-field electrospinning further facilitates user-defined custom patterning of metal oxide caterpillar-like structures.

Ultra-deep whole genome bisulfite sequencing reveals a single methylation hotspot in human brain mitochondrial DNA.

While DNA methylation is established as a major regulator of gene expression in the nucleus, the existence of mitochondrial DNA (mtDNA) methylation remains controversial. Here, we characterized the mtDNA methylation landscape in the prefrontal cortex of neurological healthy individuals (n=26) and patients with Parkinson's disease (n=27), using a combination of whole-genome bisulphite sequencing (WGBS) and bisulphite-independent methods. Accurate mtDNA mapping from WGBS data required alignment to an mtDNA reference only, to avoid misalignment to nuclear mitochondrial pseudogenes. Once correctly aligned, WGBS data provided ultra-deep mtDNA coverage (16,723 ± 7,711) and revealed overall very low levels of cytosine methylation. The highest methylation levels (5.49 ± 0.97%) were found on CpG position m.545, located in the heavy-strand promoter 1 region. The m.545 methylation was validated using a combination of methylation-sensitive DNA digestion and quantitative PCR analysis. We detected no association between mtDNA methylation profile and Parkinson's disease. Interestingly, m.545 methylation correlated with the levels of mtDNA transcripts, suggesting a putative role in regulating mtDNA gene expression. In addition, we propose a robust framework for methylation analysis of mtDNA from WGBS data, which is less prone to false-positive findings due to misalignment of nuclear mitochondrial pseudogene sequences.

The NADPARK study: A randomized phase I trial of nicotinamide riboside supplementation in Parkinson's disease.

We conducted a double-blinded phase I clinical trial to establish whether nicotinamide adenine dinucleotide (NAD) replenishment therapy, via oral intake of nicotinamide riboside (NR), is safe, augments cerebral NAD levels, and impacts cerebral metabolism in Parkinson's disease (PD). Thirty newly diagnosed, treatment-naive patients received 1,000 mg NR or placebo for 30 days. NR treatment was well tolerated and led to a significant, but variable, increase in cerebral NAD levels-measured by 31phosphorous magnetic resonance spectroscopy-and related metabolites in the cerebrospinal fluid. NR recipients showing increased brain NAD levels exhibited altered cerebral metabolism, measured by 18fluoro-deoxyglucose positron emission tomography, and this was associated with mild clinical improvement. NR augmented the NAD metabolome and induced transcriptional upregulation of processes related to mitochondrial, lysosomal, and proteasomal function in blood cells and/or skeletal muscle. Furthermore, NR decreased the levels of inflammatory cytokines in serum and cerebrospinal fluid. Our findings nominate NR as a potential neuroprotective therapy for PD, warranting further investigation in larger trials.

Metal-Metal Bonding as an Electrode Design Principle in the Low-Strain Cluster Compound LiScMo3O8.

Electrode materials for Li+-ion batteries require optimization along several disparate axes related to cost, performance, and sustainability. One of the important performance axes is the ability to retain structural integrity though cycles of charge/discharge. Metal-metal bonding is a distinct feature of some refractory metal oxides that has been largely underutilized in electrochemical energy storage, but that could potentially impact structural integrity. Here LiScMo3O8, a compound containing triangular clusters of metal-metal bonded Mo atoms, is studied as a potential anode material in Li+-ion batteries. Electrons inserted though lithiation are localized across rigid Mo3 triangles (rather than on individual metal ions), resulting in minimal structural change as suggested by operando diffraction. The unusual chemical bonding allows this compound to be cycled with Mo atoms below a formally +4 valence state, resulting in an acceptable voltage regime that is appropriate for an anode material. Several characterization methods including potentiometric entropy measurements indicate two-phase regions, which are attributed through extensive first-principles modeling to Li+ ordering. This study of LiScMo3O8 provides valuable insights for design principles for structural motifs that stably and reversibly permit Li+ (de)insertion.

Genome-wide histone acetylation analysis reveals altered transcriptional regulation in the Parkinson's disease brain.

BACKGROUND: Parkinson's disease (PD) is a complex, age-related neurodegenerative disorder of largely unknown etiology. PD is strongly associated with mitochondrial respiratory dysfunction, which can lead to epigenetic dysregulation and specifically altered histone acetylation. Nevertheless, and despite the emerging role of epigenetics in age-related brain disorders, the question of whether aberrant histone acetylation is involved in PD remains unresolved. METHODS: We studied fresh-frozen brain tissue from two independent cohorts of individuals with idiopathic PD (n = 28) and neurologically healthy controls (n = 21). We performed comprehensive immunoblotting to identify histone sites with altered acetylation levels in PD, followed by chromatin immunoprecipitation sequencing (ChIP-seq). RNA sequencing data from the same individuals was used to assess the impact of altered histone acetylation on gene expression. RESULTS: Immunoblotting analyses revealed increased acetylation at several histone sites in PD, with the most prominent change observed for H3K27, a marker of active promoters and enhancers. ChIP-seq analysis further indicated that H3K27 hyperacetylation in the PD brain is a genome-wide phenomenon with a strong predilection for genes implicated in the disease, including SNCA, PARK7, PRKN and MAPT. Integration of the ChIP-seq with transcriptomic data from the same individuals revealed that the correlation between promoter H3K27 acetylation and gene expression is attenuated in PD patients, suggesting that H3K27 acetylation may be decoupled from transcription in the PD brain. Strikingly, this decoupling was most pronounced among nuclear-encoded mitochondrial genes, corroborating the notion that impaired crosstalk between the nucleus and mitochondria is involved in the pathogenesis of PD. Our findings independently replicated in the two cohorts. CONCLUSIONS: Our findings strongly suggest that aberrant histone acetylation and altered transcriptional regulation are involved in the pathophysiology of PD. We demonstrate that PD-associated genes are particularly prone to epigenetic dysregulation and identify novel epigenetic signatures associated with the disease.

The Missing Link in the Magnetism of Hybrid Cobalt Layered Hydroxides: The Odd-Even Effect of the Organic Spacer.

A dramatic change in the magnetic behaviour, which solely depends on the parity of the organic linker molecules, has been found in a family of layered CoII hydroxides covalently functionalized with dicarboxylic molecules. These layered hybrid materials have been synthesized at room temperature using a one-pot procedure through the epoxide route. While hybrids connected by odd alkyl chains exhibit coercive fields (Hc ) below ca. 3500 Oe and show spontaneous magnetization at temperatures (TM ) below 20 K, hybrids functionalized with even alkyl chains behave as hard magnets with Hc >5500 Oe and display a TM higher than 55 K. This intriguing behaviour was studied by density functional theory with the incorporation of a Hubbard term (DFT+U) calculations, unveiling the structural subtleties underlying this observation. Indeed, the different molecular orientation exhibited by the even/odd alkyl chains, and the orientation of the covalently linked carboxylic groups modify the intensity of the magnetic coupling of both octahedral and tetrahedral in-plane sublattices, thus strongly affecting the magnetic properties of the hybrid. These findings offer an outstanding level of tuning in the molecular design of hybrid magnetic materials based on layered hydroxides.

Differential transcript usage in the Parkinson's disease brain.

Studies of differential gene expression have identified several molecular signatures and pathways associated with Parkinson's disease (PD). The role of isoform switches and differential transcript usage (DTU) remains, however, unexplored. Here, we report the first genome-wide study of DTU in PD. We performed RNA sequencing following ribosomal RNA depletion in prefrontal cortex samples of 49 individuals from two independent case-control cohorts. DTU was assessed using two transcript-count based approaches, implemented in the DRIMSeq and DEXSeq tools. Multiple PD-associated DTU events were detected in each cohort, of which 23 DTU events in 19 genes replicated across both patient cohorts. For several of these, including THEM5, SLC16A1 and BCHE, DTU was predicted to have substantial functional consequences, such as altered subcellular localization or switching to non-protein coding isoforms. Furthermore, genes with PD-associated DTU were enriched in functional pathways previously linked to PD, including reactive oxygen species generation and protein homeostasis. Importantly, the vast majority of genes exhibiting DTU were not differentially expressed at the gene-level and were therefore not identified by conventional differential gene expression analysis. Our findings provide the first insight into the DTU landscape of PD and identify novel disease-associated genes. Moreover, we show that DTU may have important functional consequences in the PD brain, since it is predicted to alter the functional composition of the proteome. Based on these results, we propose that DTU analysis is an essential complement to differential gene expression studies in order to provide a more accurate and complete picture of disease-associated transcriptomic alterations.

Meta-analysis of whole-exome sequencing data from two independent cohorts finds no evidence for rare variant enrichment in Parkinson disease associated loci.

Parkinson disease (PD) is a complex neurodegenerative disorder influenced by both environmental and genetic factors. While genome wide association studies have identified several susceptibility loci, many causal variants and genes underlying these associations remain undetermined. Identifying these is essential in order to gain mechanistic insight and identify biological pathways that may be targeted therapeutically. We hypothesized that gene-based enrichment of rare mutations is likely to be found within susceptibility loci for PD and may help identify causal genes. Whole-exome sequencing data from two independent cohorts were analyzed in tandem and by meta-analysis and a third cohort genotyped using the NeuroX-array was used for replication analysis. We employed collapsing methods (burden and the sequence kernel association test) to detect gene-based enrichment of rare, protein-altering variation within established PD susceptibility loci. Our analyses showed trends for three genes (GALC, PARP9 and SEC23IP), but none of these survived multiple testing correction. Our findings provide no evidence of rare mutation enrichment in genes within PD-associated loci, in our datasets. While not excluding that rare mutations in these genes may influence the risk of idiopathic PD, our results suggest that, if such effects exist, much larger sequencing datasets will be required for their detection.

Synergy of Electrostatic and π-π Interactions in the Realization of Nanoscale Artificial Photosynthetic Model Systems.

In the scientific race to build up photoactive electron donor-acceptor systems with increasing efficiencies, little is known about the interplay of their building blocks when integrated into supramolecular nanoscale arrays, particularly in aqueous environments. Here, we describe an aqueous donor-acceptor ensemble whose emergence as a nanoscale material renders it remarkably stable and efficient. We have focused on a tetracationic zinc phthalocyanine (ZnPc) featuring pyrenes, which shows an unprecedented mode of aggregation, driven by subtle cooperation between electrostatic and π-π interactions. Our studies demonstrate monocrystalline growth in solution and a symmetry-breaking intermolecular charge transfer between adjacent ZnPcs upon photoexcitation. Immobilizing a negatively charged fullerene (C60 ) as electron acceptor onto the monocrystalline ZnPc assemblies was found to enhance the overall stability, and to suppress the energy-wasting charge recombination found in the absence of C60 . Overall, the resulting artificial photosynthetic model system exhibits a high degree of preorganization, which facilitates efficient charge separation and subsequent charge transport.

Mitochondrial respiratory chain deficiency correlates with the severity of neuropathology in sporadic Creutzfeldt-Jakob disease.

Mitochondrial dysfunction has been implicated in multiple neurodegenerative diseases but remains largely unexplored in Creutzfeldt-Jakob disease. Here, we characterize the mitochondrial respiratory chain at the individual neuron level in the MM1 and VV2 common molecular subtypes of sporadic Creutzfeldt-Jakob disease. Moreover, we investigate the associations between the mitochondrial respiratory chain and neuropathological markers of the disease.Brain tissue from individuals with sporadic Creutzfeldt-Jakob disease and age-matched controls were obtained from the brain collection of the Austrian Creutzfeldt-Jakob Surveillance. The mitochondrial respiratory chain was studied through a dichotomous approach of immunoreactivities in the temporal cortex and the hippocampal subregions of CA4 and CA3.We show that profound deficiency of all mitochondrial respiratory complexes (I-V) occurs in neurons of the severely affected temporal cortex of patients with Creutzfeldt-Jakob disease. This deficiency correlates strongly with the severity of neuropathological changes, including vacuolation of the neuropil, gliosis and disease associated prion protein load. Respiratory chain deficiency is less pronounced in hippocampal CA4 and CA3 regions compared to the temporal cortex. In both areas respiratory chain deficiency shows a predilection for the MM1 molecular subtype of Creutzfeldt-Jakob disease.Our findings indicate that aberrant mitochondrial respiration could be involved early in the pathogenesis of sporadic Creutzfeldt-Jakob disease and contributes to neuronal death, most likely via ATP depletion. Based on these results, we propose that the restricted MRI diffusion profile seen in the brain of patients with sporadic Creutzfeldt-Jakob disease might reflect cytotoxic changes due to neuronal respiratory chain failure and ATP loss.

Low energy nano diffraction (LEND) - A versatile diffraction technique in SEM.

Electron diffraction is a powerful characterization method that is used across different fields and in different instruments. In particular, the power of transmission electron microscopy (TEM) largely relies on the capability to switch between imaging and diffraction mode enabling identification of crystalline phases and in-depth studies of crystal defects, to name only examples. In contrast, while diffraction techniques have found their way into the realm of scanning electron microscopy (SEM) in the form of electron backscatter diffraction and related techniques, on-axis transmission diffraction is still in its infancy. Here we present a simple but versatile setup that enables a 'diffraction mode' in SEM using a fluorescent screen and a dedicated in vacuo camera. With this setup spot-like nano-beam diffraction patterns of thin samples can be acquired with electron energies as low as 500 eV. We therefore coin the name Low Energy Nano Diffraction (LEND). Diffraction patterns can be recorded from single positions on the sample or integrated over selected areas by adjustable scan patterns. Besides showing the principal application of the technique to standard materials such as gold and silicon we also explore the application to graphene and other 2D materials. Besides single pattern measurements, also full 4D-STEM diffraction mappings are demonstrated. Finally, we show how the integration of a versatile diffraction mode in SEM enables a thorough analysis performed with a single instrument.

Mechanical cleaning of graphene using in situ electron microscopy.

Avoiding and removing surface contamination is a crucial task when handling specimens in any scientific experiment. This is especially true for two-dimensional materials such as graphene, which are extraordinarily affected by contamination due to their large surface area. While many efforts have been made to reduce and remove contamination from such surfaces, the issue is far from resolved. Here we report on an in situ mechanical cleaning method that enables the site-specific removal of contamination from both sides of two dimensional membranes down to atomic-scale cleanliness. Further, mechanisms of re-contamination are discussed, finding surface-diffusion to be the major factor for contamination in electron microscopy. Finally the targeted, electron-beam assisted synthesis of a nanocrystalline graphene layer by supplying a precursor molecule to cleaned areas is demonstrated.

Poly-ADP-ribose assisted protein localization resolves that DJ-1, but not LRRK2 or α-synuclein, is localized to the mitochondrial matrix.

Several proteins linked to familial Parkinson disease have been associated with mitochondrial (dys-)function and have been described to reside within mitochondria. The putative mitochondrial and sub-mitochondrial localization of these proteins remains disputed, however, potentially due to conflicting results obtained by diverging technical approaches. Using the high-resolution poly-ADP-ribose assisted protein localization assay that also allows for detection of low level and even partial mitochondrial matrix localization, we demonstrate here that DJ-1, but not LRRK2 or α-synuclein, resides in the mitochondrial matrix. The localization of the proteins was not changed in cellular stress models of Parkinson disease and, in case of α-synuclein, not affected by pathological mutations. Our results verify the ability of DJ-1 to carry out its role also from within mitochondria and suggest that LRRK2 and α-synuclein may interact with and affect mitochondria from outside the mitochondrial matrix.

In situ manipulation and switching of dislocations in bilayer graphene.

Topological defects in crystalline solids are of fundamental interest in physics and materials science because they can radically alter the properties of virtually any material. Of particular importance are line defects, known as dislocations, which are the main carriers of plasticity and have a tremendous effect on electronic and optical properties. Understanding and controlling the occurrence and behavior of those defects have been of major and ongoing interest since their discovery in the 1930s. This interest was renewed with the advent of two-dimensional materials in which a single topological defect can alter the functionality of the whole system and even create new physical phenomena. We present an experimental approach to directly manipulate dislocations in situ on the nanometer scale by using a dedicated scanning electron microscope setup. With this approach, key fundamental characteristics such as line tension, defect interaction, and node formation have been studied. A novel switching reaction, based on the recombination of dislocation lines, was found, which paves the way for the concept of switches made of a bimodal topological defect configuration.