The African killifish: A short-lived vertebrate model to study the biology of sarcopenia and longevity.

Sarcopenia, the age-related decline in muscle function, places a considerable burden on health-care systems. While the stereotypic hallmarks of sarcopenia are well characterized, their contribution to muscle wasting remains elusive, which is partly due to the limited availability of animal models. Here, we have performed cellular and molecular characterization of skeletal muscle from the African killifish-an extremely short-lived vertebrate-revealing that while many characteristics deteriorate with increasing age, supporting the use of killifish as a model for sarcopenia research, some features surprisingly reverse to an "early-life" state in the extremely old stages. This suggests that in extremely old animals, there may be mechanisms that prevent further deterioration of skeletal muscle, contributing to an extension of life span. In line with this, we report a reduction in mortality rates in extremely old killifish. To identify mechanisms for this phenomenon, we used a systems metabolomics approach, which revealed that during aging there is a striking depletion of triglycerides, mimicking a state of calorie restriction. This results in the activation of mitohormesis, increasing Sirt1 levels, which improves lipid metabolism and maintains nutrient homeostasis in extremely old animals. Pharmacological induction of Sirt1 in aged animals was sufficient to induce a late life-like metabolic profile, supporting its role in life span extension in vertebrate populations that are naturally long-lived. Collectively, our results demonstrate that killifish are not only a novel model to study the biological processes that govern sarcopenia, but they also provide a unique vertebrate system to dissect the regulation of longevity.

Explaining Variation in Individual Aging, Its Sources, and Consequences: A Comprehensive Conceptual Model of Human Aging.

We define aging as a characteristic deterioration in one (or more) observable attributes of an organism that typically occurs during later life. With this narrow functional definition, we gain the freedom to separate aging from other processes of age-related change (e.g., maturation, growth, illness, terminal decline). We introduce a structural model that distinguishes between (1) the phenomenon of aging, (2) the subjective experience of aging, (3) sources of aging, and (4) consequences of aging. A core focus of the model is on the role of buffering mechanisms of biological repair and personal adaptation that regulate the relations between sources of aging, aging proper, and its consequences. The quality and level of functioning of these buffering mechanisms also varies across the life span, which directly affects the sources of aging, resulting in either resilience against or accelerated aging, and thus can be considered to be a major source of the variation in aging processes among different individuals. External factors comprising attributes of the physical environment and sociocultural characteristics are considered as contexts in which aging occurs. These contextual factors are assumed to feed into the various components of the model. Our model provides an interdisciplinary account of human aging, its sources and consequences, and also its subjective experience, by integrating biological, psychological, lifestyle, and sociocultural factors, and by specifying their interrelations and interactions. The model provides a comprehensive understanding of individual human aging, its underlying processes, and modulating factors. It allows for the derivation of empirically testable hypotheses, and it helps practitioners to identify elements that lend themselves to targeted intervention efforts aimed at increasing the resilience of individuals against aging and buffering its negative consequences.

The Ionospheric Connection Explorer - Prime Mission Review.

The two-year prime mission of the NASA Ionospheric Connection Explorer (ICON) is complete. The baseline operational and scientific objectives have been met and exceeded, as detailed in this report. In October of 2019, ICON was launched into an orbit that provides its instruments the capability to deliver near-continuous measurements of the densest plasma in Earth's space environment. Through collection of a key set of in-situ and remote sensing measurements that are, by virtue of a detailed mission design, uniquely synergistic, ICON enables completely new investigations of the mechanisms that control the behavior of the ionosphere-thermosphere system under both geomagnetically quiet and active conditions. In a two-year period that included a deep solar minimum, ICON has elucidated a number of remarkable effects in the ionosphere attributable to energetic inputs from the lower and middle atmosphere, and shown how these are transmitted from the edge of space to the peak of plasma density above. The observatory operated in a period of low activity for 2 years and then for a year with increasing solar activity, observing the changing balance of the impacts of lower and upper atmospheric drivers on the ionosphere.

Michelson Interferometer for Global High-Resolution Thermospheric Imaging (MIGHTI) On-Orbit Wind Observations: Data Analysis and Instrument Performance.

The design, principles of operation, calibration, and data analysis approaches of the Michelson Interferometer for Global High-resolution Thermospheric Imaging (MIGHTI) on the NASA Ionospheric Connection (ICON) satellite have been documented prior to the ICON launch. Here we update and expand on the MIGHTI wind data analysis and discuss the on-orbit instrument performance. In particular, we show typical raw data and we describe key processing steps, including the correction of a "signal-intensity dependent phase shift," which is necessitated by unexpected detector behavior. We describe a new zero-wind calibration approach that is preferred over the originally planned approach due to its higher precision. Similar to the original approach, the new approach is independent of any a priori data. A detailed update on the wind uncertainties is provided and compared to the mission requirements, showing that MIGHTI has met the ICON mission requirements. While MIGHTI observations are not required to produce absolute airglow brightness profiles, we describe a relative brightness profile product, which is included in the published data. We briefly review the spatial resolution of the MIGHTI wind data in addition to the data coverage and data gaps that occurred during the nominal mission. Finally, we include comparisons of the MIGHTI wind data with ground-based Fabry-Perot interferometer observations and meteor radar observations, updating previous studies with more recent data, again showing good agreement. The data processing steps covered in this work and all the derived wind data correspond to the MIGHTI data release Version 5 (v05).

Generation of a transparent killifish line through multiplex CRISPR/Cas9mediated gene inactivation.

Body pigmentation is a limitation for in vivo imaging and thus for the performance of longitudinal studies in biomedicine. A possibility to circumvent this obstacle is the employment of pigmentation mutants, which are used in fish species like zebrafish and medaka. To address the basis of aging, the short-lived African killifish Nothobranchius furzeri has recently been established as a model organism. Despite its short lifespan, N. furzeri shows typical signs of mammalian aging including telomere shortening, accumulation of senescent cells, and loss of regenerative capacity. Here, we report the generation of a transparent N. furzeri line by the simultaneous inactivation of three key loci responsible for pigmentation. We demonstrate that this stable line, named klara, can serve as a tool for different applications including behavioral experiments and the establishment of a senescence reporter by integration of a fluorophore into the cdkn1a (p21) locus and in vivo microscopy of the resulting line.

Rapid Genotyping of Nothobranchius furzeri Embryos, Larvae, and Adult Fish via High-Resolution Melt Analysis (HRMA).

CRISPR-Cas9 has eased the induction of sequence-specific mutations and has therefore become a powerful tool to generate mutant lines for studying the role of specific genes. The cellular repair of Cas9-induced double-stranded DNA breaks by the error-prone nonhomologous end-joining pathway can result in various indel mutations. Having identified and chosen a specific mutation in a target gene, the establishment of a respective mutant line requires a feasible and precise method to differentiate the genotypes of the offspring. Here, we provide a protocol that allows genotyping of large numbers of Nothobranchius furzeri embryos, larvae, and adults harboring a previously identified indel or point mutation in a short time via high-resolution melt analysis (HRMA).

Adapting the pantograph limb: Differential robustness of fore- and hindlimb kinematics against genetically induced perturbation in the neural control networks and its evolutionary implications.

The evolutionary transformation of limb morphology to the four-segmented pantograph of therians is among the milestones of mammalian evolution. But, it is still unknown if changes of the mechanical limb function were accompanied by corresponding changes in development and sensorimotor control. The impressive locomotor performance of mammals leaves no doubt about the high integration of pattern formation, neural control and mechanics. But, deviations from normal intra- and interlimb coordination (spatial and temporal) become evident in the presence of perturbations. We induced a perturbation in the development of the neural circuits of the spinal cord of mice (Mus musculus) using a deletion of the Wilms tumor suppressor gene Wt1 in a subpopulation of dI6 interneurons. These interneurons are assumed to participate in the intermuscular coordination within the limb and in left-right-coordination between the limbs. We describe the locomotor kinematics in mice with conditional Wt1 knockout and compare them to mice without Wt1 deletion. Unlike knockout neonates, knockout adult mice do not display severe deviations from normal (=control group) interlimb coordination, but the coordinated protraction and retraction of the limbs is altered. The forelimbs are more affected by deviations from the control than the hindlimbs. This observation appears to reflect a different degree of integration and resistance against the induced perturbation between the limbs. Interestingly, the observed effects are similar to locomotor deficits reported to arise when sensory feedback from proprioceptors or cutaneous receptors is impaired. A putative participation of Wt1 positive dI6 interneurons in sensorimotor integration is therefore considered.

Sex chromosome differentiation via changes in the Y chromosome repeat landscape in African annual killifishes Nothobranchius furzeri and N. kadleci.

Homomorphic sex chromosomes and their turnover are common in teleosts. We investigated the evolution of nascent sex chromosomes in several populations of two sister species of African annual killifishes, Nothobranchius furzeri and N. kadleci, focusing on their under-studied repetitive landscape. We combined bioinformatic analyses of the repeatome with molecular cytogenetic techniques, including comparative genomic hybridization, fluorescence in situ hybridization with satellite sequences, ribosomal RNA genes (rDNA) and bacterial artificial chromosomes (BACs), and immunostaining of SYCP3 and MLH1 proteins to mark lateral elements of synaptonemal complexes and recombination sites, respectively. Both species share the same heteromorphic XY sex chromosome system, which thus evolved prior to their divergence. This was corroborated by sequence analysis of a putative master sex determining (MSD) gene gdf6Y in both species. Based on their divergence, differentiation of the XY sex chromosome pair started approximately 2 million years ago. In all populations, the gdf6Y gene mapped within a region rich in satellite DNA on the Y chromosome long arms. Despite their heteromorphism, X and Y chromosomes mostly pair regularly in meiosis, implying synaptic adjustment. In N. kadleci, Y-linked paracentric inversions like those previously reported in N. furzeri were detected. An inversion involving the MSD gene may suppress occasional recombination in the region, which we otherwise evidenced in the N. furzeri population MZCS-121 of the Limpopo clade lacking this inversion. Y chromosome centromeric repeats were reduced compared with the X chromosome and autosomes, which points to a role of relaxed meiotic drive in shaping the Y chromosome repeat landscape. We speculate that the recombination rate between sex chromosomes was reduced due to heterochiasmy. The observed differences between the repeat accumulations on the X and Y chromosomes probably result from high repeat turnover and may not relate closely to the divergence inferred from earlier SNP analyses.

Molecular Sexing of Nothobranchius furzeri Embryos and Larvae.

Differences between the sexes are of increasing interest in basic and applied research with regard to development, behavior, aging, and diseases. Although the African turquoise killifish Nothobranchius furzeri, a model for aging research well known for its remarkably short life span, develops strong sexual dimorphism in adulthood, there is no visible indicator of its sex in embryonic and juvenile stages. To address this issue, we developed a molecular sexing assay exploiting two large sequence polymorphisms in the minimal sex-determining region (SDR) of N. furzeri These polymorphisms are sequence deletions on the Y chromosome that involve the lack or truncation of one or multiple microsatellites. The simple polymerase chain reaction (PCR) readout of the assays described here allows the sexing of N. furzeri embryos and larvae in a medium- to high-throughput and cost-efficient manner.

IRC-Safe Graph Autoencoder for Unsupervised Anomaly Detection.

Anomaly detection through employing machine learning techniques has emerged as a novel powerful tool in the search for new physics beyond the Standard Model. Historically similar to the development of jet observables, theoretical consistency has not always assumed a central role in the fast development of algorithms and neural network architectures. In this work, we construct an infrared and collinear safe autoencoder based on graph neural networks by employing energy-weighted message passing. We demonstrate that whilst this approach has theoretically favorable properties, it also exhibits formidable sensitivity to non-QCD structures.

Exospheric Temperature Measured by NASA-GOLD Under Low Solar Activity: Comparison With Other Data Sets.

Exospheric temperature is one of the key parameters in constructing thermospheric models and has been extensively studied with in situ observations and remote sensing. The Global-scale Observations of the Limb and Disk (GOLD) at a geosynchronous vantage point provides dayglow limb images for two longitude sectors, from which we can estimate the terrestrial exospheric temperature since 2018. In this paper, we investigate climatological behavior of the exospheric temperature measured by GOLD. The temperature has positive correlations with solar and geomagnetic activity and exhibits a morning-afternoon asymmetry, both of which agree with previous studies. We have found that the arithmetic sum of F10.7 (solar) and Ap (geomagnetic) indices is highly correlated with the exospheric temperature, explaining ∼64% of the day-to-day variability. Furthermore, the exospheric temperature has good correlation with thermospheric parameters (e.g., neutral temperature, O2 density, and NO emission index) sampled at various heights above ∼130 km, in spite of the well-known thermal gradient below ∼200 km. However, thermospheric temperature at altitudes around 100 km is not well correlated with the GOLD exospheric temperature. The result implies that effects other than thermospheric heating by solar Extreme Ultraviolet and geomagnetic activity take control below a threshold altitude that exists between ∼100 and ∼130 km.

Wt1 transcription factor impairs cardiomyocyte specification and drives a phenotypic switch from myocardium to epicardium.

During development, the heart grows by addition of progenitor cells to the poles of the primordial heart tube. In the zebrafish, Wilms tumor 1 transcription factor a (wt1a) and b (wt1b) genes are expressed in the pericardium, at the venous pole of the heart. From this pericardial layer, the proepicardium emerges. Proepicardial cells are subsequently transferred to the myocardial surface and form the epicardium, covering the myocardium. We found that while wt1a and wt1b expression is maintained in proepicardial cells, it is downregulated in pericardial cells that contributes cardiomyocytes to the developing heart. Sustained wt1b expression in cardiomyocytes reduced chromatin accessibility of specific genomic loci. Strikingly, a subset of wt1a- and wt1b-expressing cardiomyocytes changed their cell-adhesion properties, delaminated from the myocardium and upregulated epicardial gene expression. Thus, wt1a and wt1b act as a break for cardiomyocyte differentiation, and ectopic wt1a and wt1b expression in cardiomyocytes can lead to their transdifferentiation into epicardial-like cells.

Aging Activates the Immune System and Alters the Regenerative Capacity in the Zebrafish Heart.

Age-associated organ failure and degenerative diseases have a major impact on human health. Cardiovascular dysfunction has an increasing prevalence with age and is one of the leading causes of death. In contrast to humans, zebrafish have extraordinary regeneration capacities of complex organs including the heart. In addition, zebrafish has recently become a model organism in research on aging. Here, we have compared the ventricular transcriptome as well as the regenerative capacity after cryoinjury of old and young zebrafish hearts. We identified the immune system as activated in old ventricles and found muscle organization to deteriorate upon aging. Our data show an accumulation of immune cells, mostly macrophages, in the old zebrafish ventricle. Those immune cells not only increased in numbers but also showed morphological and behavioral changes with age. Our data further suggest that the regenerative response to cardiac injury is generally impaired and much more variable in old fish. Collagen in the wound area was already significantly enriched in old fish at 7 days post injury. Taken together, these data indicate an 'inflammaging'-like process in the zebrafish heart and suggest a change in regenerative response in the old.

Evaluation of Atmospheric 3-Day Waves as a Source of Day-to-Day Variation of the Ionospheric Longitudinal Structure.

We report for the first time the day-to-day variation of the longitudinal structure in height of the F2 layer (hmF2) in the equatorial ionosphere using multi-satellite observations of electron density profiles by the Constellation Observing System for Meteorology, Ionosphere and Climate-2 (COSMIC-2). These observations reveal a ~3-day modulation of the hmF2 wavenumber-4 structure viewed in a fixed local time frame during January 30-February 14, 2021. Simultaneously, ~3-day planetary wave activity is discerned from zonal wind observations at ~100 km by the Ionospheric Connection Explorer (ICON) Michelson Interferometer for Global High-Resolution Thermospheric Imaging (MIGHTI). This signature is not observed at ~180-250 km altitudes, suggesting the dissipation of this wave below the F-region. We propose that the 3-day variation identified in h mF2 is likely caused by the planetary wave-tide interaction through the E-region dynamo.

Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.

Neurodegenerative diseases, including Alzheimer's (AD) and Parkinson's diseases (PD), are complex heterogeneous diseases with highly variable patient responses to treatment. Due to the growing evidence for ageing-related clinical and pathological commonalities between AD and PD, these diseases have recently been studied in tandem. In this study, we analysed transcriptomic data from AD and PD patients, and stratified these patients into three subclasses with distinct gene expression and metabolic profiles. Through integrating transcriptomic data with a genome-scale metabolic model and validating our findings by network exploration and co-analysis using a zebrafish ageing model, we identified retinoids as a key ageing-related feature in all subclasses of AD and PD. We also demonstrated that the dysregulation of androgen metabolism by three different independent mechanisms is a source of heterogeneity in AD and PD. Taken together, our work highlights the need for stratification of AD/PD patients and development of personalised and precision medicine approaches based on the detailed characterisation of these subclasses.

Atmosphere-Ionosphere (A-I) Coupling as Viewed by ICON: Day-to-Day Variability Due to Planetary Wave (PW)-Tide Interactions.

Coincident Ionospheric Connections Explorer (ICON) measurements of neutral winds, plasma drifts and total ion densities (:=Ne, electron density) are analyzed during January 1-21, 2020 to reveal the relationship between neutral winds and ionospheric variability on a day-to-day basis. Atmosphere-ionosphere (A-I) connectivity inevitably involves a spectrum of planetary waves (PWs), tides and secondary waves due to wave-wave nonlinear interactions. To provide a definitive attribution of dynamical origins, the current study focuses on a time interval when the longitudinal wave-4 component of the E-region winds is dominated by the eastward-propagating diurnal tide with zonal wavenumber s = -3 (DE3). DE3 is identified in winds and ionospheric parameters through its characteristic dependence on local solar time and longitude as ICON's orbit precesses. Superimposed on this trend are large variations in low-latitude DE3 wave-4 zonal winds (±40 ms-1) and topside F-region equatorial vertical drifts at periods consistent with 2-days and 6-days PWs, and a ~3-day ultra-fast Kelvin wave (UFKW), coexisting during this time interval; the DE3 winds, dynamo electric fields, and drifts are modulated by these waves. Wave-4 variability in Ne is of order 25%-35%, but the origins are more complex, likely additionally reflecting transport by ~20-25 ms-1 wave-4 in-situ winds containing strong signatures of DE3 interactions with ambient diurnal Sun-synchronous winds and ion drag. These results are the first to show a direct link between day-to-day wave-4 variability in contemporaneously measured E-region neutral winds and F-region ionospheric drifts and electron densities.

First results from the retrieved column O/N2 ratio from the Ionospheric Connection Explorer (ICON): Evidence of the impacts of nonmigrating tides.

In near-Earth space, variations in thermospheric composition have important implications for thermosphere-ionosphere coupling. The ratio of O to N2 is often measured using far-UV airglow observations. Taking such airglow observations from space, looking below the Earth's limb allows for the total column of O and N2 in the ionosphere to be determined. While these observations have enabled many previous studies, determining the impact of non-migrating tides on thermospheric composition has proved difficult, owing to a small contamination of the signal by recombination of ionospheric O+. New ICON observations of far UV are presented here, and their general characteristics are shown. Using these, along with other observations and a global circulation model we show that during the morning hours and at latitudes away from the peak of the equatorial ionospheric anomaly, the impact of non-migrating tides on thermospheric composition can be observed. During March - April 2020, the column O/N2 ratio was seen to vary by 3 - 4 % of the zonal mean. By comparing the amplitude of the variation observed with that in the model, both the utility of these observations and a pathway to enable future studies is shown.

Isolated Peak of Oxygen Ion Fraction in the Post-Noon Equatorial F-Region: ICON and SAMI3/WACCM-X.

In the equatorial region, the fraction of oxygen ions (O+) in the topside ionosphere contains information on the source altitude of the plasma, which is controlled, in part, by the vertical plasma motion in the F-region. Previous studies on this topic are restricted by limited coverage of local time, latitude, and season, leaving a significant knowledge gap in the distribution of the topside ionospheric composition. In this study, we statistically investigate the O+ fraction measured by ICON/IVM over all the local time sectors and seasons at low/midlatitudes. For the first time, we have found that an isolated peak in the O+ fraction emerges in the post-noon equatorial region. The peak is most prominent during equinoxes, while during solstices it is connected to the O+ fraction bulges in the local summer midlatitudes. Simulations with SAMI3 coupled with thermospheric parameters from WACCM-X reproduce the peak of the O+ fraction. The post-noon equatorial peak can be explained by the net vertical motion of plasma consisting of transports either parallel or perpendicular to geomagnetic field lines.

Validation of ICON-MIGHTI Thermospheric Wind Observations: 2. Green-Line Comparisons to Specular Meteor Radars.

We compare coincident thermospheric neutral wind observations made by the Michelson Interferometer for Global High-Resolution Thermospheric Imaging (MIGHTI) on the Ionospheric Connection Explorer (ICON) spacecraft, and four ground-based specular meteor radars (SMRs). Using the green-line MIGHTI channel, we analyze 1158 coincidences between Dec 2019 and May 2020 in the altitude range from 94 to 104 km where the observations overlap. We find that the two datasets are strongly correlated (r = 0.82) with a small mean difference (4.5 m/s). Although this agreement is good, an analysis of known error sources (e.g., shot noise, calibration errors, and analysis assumptions) can only account for about a quarter of the disagreement variance. The unexplained variance is 27.8% of the total signal variance and could be caused by unknown errors. However, based on an analysis of the spatial and caused by temporal variability of the wind on scales ≲70 min. The observed magnitudes agree well during temporal averaging of the two measurement modalities, we suggest that some of the disagreement is likely the night, but during the day, MIGHTI observes 16%-25% faster winds than the SMRs. This remains unresolved but is similar in certain ways to previous SMR-satellite comparisons.