Telomeres and aging: on and off the planet!

Improving human healthspan in our rapidly aging population has never been more imperative. Telomeres, protective "caps" at the ends of linear chromosomes, are essential for maintaining genome stability of eukaryotic genomes. Due to their physical location and the "end-replication problem" first envisioned by Dr. Alexey Olovnikov, telomeres shorten with cell division, the implications of which are remarkably profound. Telomeres are hallmarks and molecular drivers of aging, as well as fundamental integrating components of the cumulative effects of genetic, lifestyle, and environmental factors that erode telomere length over time. Ongoing telomere attrition and the resulting limit to replicative potential imposed by cellular senescence serves a powerful tumor suppressor function, and also underlies aging and a spectrum of age-related degenerative pathologies, including reduced fertility, dementias, cardiovascular disease and cancer. However, very little data exists regarding the extraordinary stressors and exposures associated with long-duration space exploration and eventual habitation of other planets, nor how such missions will influence telomeres, reproduction, health, disease risk, and aging. Here, we briefly review our current understanding, which has advanced significantly in recent years as a result of the NASA Twins Study, the most comprehensive evaluation of human health effects associated with spaceflight ever conducted. Thus, the Twins Study is at the forefront of personalized space medicine approaches for astronauts and sets the stage for subsequent missions. We also extrapolate from current understanding to future missions, highlighting potential biological and biochemical strategies that may enable human survival, and consider the prospect of longevity in the extreme environment of space.

Genome and clonal hematopoiesis stability contrasts with immune, cfDNA, mitochondrial, and telomere length changes during short duration spaceflight.

Background: The Inspiration4 (I4) mission, the first all-civilian orbital flight mission, investigated the physiological effects of short-duration spaceflight through a multi-omic approach. Despite advances, there remains much to learn about human adaptation to spaceflight's unique challenges, including microgravity, immune system perturbations, and radiation exposure. Methods: To provide a detailed genetics analysis of the mission, we collected dried blood spots pre-, during, and post-flight for DNA extraction. Telomere length was measured by quantitative PCR, while whole genome and cfDNA sequencing provided insight into genomic stability and immune adaptations. A robust bioinformatic pipeline was used for data analysis, including variant calling to assess mutational burden. Result: Telomere elongation occurred during spaceflight and shortened after return to Earth. Cell-free DNA analysis revealed increased immune cell signatures post-flight. No significant clonal hematopoiesis of indeterminate potential (CHIP) or whole-genome instability was observed. The long-term gene expression changes across immune cells suggested cellular adaptations to the space environment persisting months post-flight. Conclusion: Our findings provide valuable insights into the physiological consequences of short-duration spaceflight, with telomere dynamics and immune cell gene expression adapting to spaceflight and persisting after return to Earth. CHIP sequencing data will serve as a reference point for studying the early development of CHIP in astronauts, an understudied phenomenon as previous studies have focused on career astronauts. This study will serve as a reference point for future commercial and non-commercial spaceflight, low Earth orbit (LEO) missions, and deep-space exploration.

Monitoring Genomic Structural Rearrangements Resulting from Gene Editing.

The cytogenomics-based methodology of directional genomic hybridization (dGH) enables the detection and quantification of a more comprehensive spectrum of genomic structural variants than any other approach currently available, and importantly, does so on a single-cell basis. Thus, dGH is well-suited for testing and/or validating new advancements in CRISPR-Cas9 gene editing systems. In addition to aberrations detected by traditional cytogenetic approaches, the strand specificity of dGH facilitates detection of otherwise cryptic intra-chromosomal rearrangements, specifically small inversions. As such, dGH represents a powerful, high-resolution approach for the quantitative monitoring of potentially detrimental genomic structural rearrangements resulting from exposure to agents that induce DNA double-strand breaks (DSBs), including restriction endonucleases and ionizing radiations. For intentional genome editing strategies, it is critical that any undesired effects of DSBs induced either by the editing system itself or by mis-repair with other endogenous DSBs are recognized and minimized. In this paper, we discuss the application of dGH for assessing gene editing-associated structural variants and the potential heterogeneity of such rearrangements among cells within an edited population, highlighting its relevance to personalized medicine strategies.

Medical education: Accommodating students with ADHD.

Attention-Deficit/Hyperactivity Disorder (ADHD) is a neurodevelopmental disorder that affects a significant number of medical students worldwide. It is poorly recognised by educators, and therefore inadequately accommodated for in educational strategies. In order to investigate this further, a literature review and pilot survey were conducted. Health educators employed by The University of Newcastle, Australia, completed a short online survey, which focused on their understanding of, and ability to recognise and adapt teaching strategies for students with ADHD. The results of the survey informed the development of a resource that provided evidence-based strategies for supporting the learning of tertiary students with ADHD. In addition, the results of this pilot study may form the basis for further research in this domain. Given the prevalence and potential impact of ADHD on higher education, it is important to gain deeper insight into how medical educators can best engage and support students with ADHD. This knowledge may potentially reduce the negative impacts of this neurodiversity on students and support their learning and well-being throughout their medical career. Ultimately this may help doctors to achieve their full potential, especially in clinical decision-making.

Arabidopsis telomerase takes off by uncoupling enzyme activity from telomere length maintenance in space.

Spaceflight-induced changes in astronaut telomeres have garnered significant attention in recent years. While plants represent an essential component of future long-duration space travel, the impacts of spaceflight on plant telomeres and telomerase have not been examined. Here we report on the telomere dynamics of Arabidopsis thaliana grown aboard the International Space Station. We observe no changes in telomere length in space-flown Arabidopsis seedlings, despite a dramatic increase in telomerase activity (up to 150-fold in roots), as well as elevated genome oxidation. Ground-based follow up studies provide further evidence that telomerase is induced by different environmental stressors, but its activity is uncoupled from telomere length. Supporting this conclusion, genetically engineered super-telomerase lines with enhanced telomerase activity maintain wildtype telomere length. Finally, genome oxidation is inversely correlated with telomerase activity levels. We propose a redox protective capacity for Arabidopsis telomerase that may promote survivability in harsh environments.

Exploring the Relationship between Spontaneous Sister Chromatid Exchange and Genome Instability in Two Cryptic Species of Non-Human Primates.

There are extensive studies on chromosome morphology and karyotype diversity in primates, yet we still lack insight into genomic instability as a key factor underlying the enormous interspecies chromosomal variability and its potential contribution to evolutionary dynamics. In this sense, the assessment of spontaneous sister chromatid exchange (SCE) frequencies represents a powerful tool for evaluating genome stability. Here, we employed G-banding, fluorescence plus Giemsa (FPG), and chromosome orientation fluorescence in situ hybridization (CO-FISH) methodologies to characterize both chromosome-specific frequencies of spontaneously occurring SCE throughout the genome (G-SCE) and telomere-specific SCE (T-SCE). We analyzed primary fibroblast cultures from two male species of Ateles living in captivity: Ateles paniscus (APA) and Ateles chamek (ACH). High frequencies of G-SCEs were observed in both species. Interestingly, G-SCEs clustered on evolutionary relevant chromosome pairs: ACH chromosomes 1, 2, 3, 4, and 7, and APA chromosomes 1, 2, 3, 4/12, 7, and 10. Furthermore, a statistically significant difference between the observed and expected G-SCE frequencies, not correlated with chromosome size, was also detected. CO-FISH analyses revealed the presence of telomere-specific recombination events in both species, which included T-SCE, as well as interstitial telomere signals and telomere duplications, with APA chromosomes displaying higher frequencies, compared to ACH. Our analyses support the hypothesis that regions of Ateles chromosomes susceptible to recombination events are fragile sites and evolutionary hot spots. Thus, we propose SCE analyses as a valuable indicator of genome instability in non-human primates.

Towards evolutionary predictions: Current promises and challenges.

Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ. For example, we could try to predict which genotype will dominate, the fitness of the population or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by establishing a common language for evolutionary predictions.

Modeling optimal reopening strategies for COVID-19 and its variants by keeping infections low and fixing testing capacity.

Since early March 2020, government agencies have utilized a wide variety of non-pharmaceutical interventions to mitigate the spread of COVID-19 and have struggled to determine when it is appropriate to return to in-person activities after an outbreak is detected. At many universities, fundamental issues related to understanding the spread of the disease (e.g. the transmission rate), the ability of administrators to respond quickly enough by closing when there is a sudden rise in cases, and how to make a decision on when to reopen remains a concern. Surveillance testing strategies have been implemented in some places, and those test outcomes have dictated whether to reopen, to simultaneously monitor community spread, and/or to isolate discovered cases. However, the question remains as to when it is safe to reopen and how much testing is required to remain safely open while keeping infection numbers low. Here, we propose an extension of the classic SIR model to investigate reopening strategies for a fixed testing strategy, based on feedback from testing results. Specifically, we close when a predefined proportion of the population becomes infected, and later reopen when that infected proportion decreases below a predefined threshold. A valuable outcome of our approach is that our reopening strategies are robust to variation in almost all model parameters, including transmission rates, which can be extremely difficult to determine as they typically differ between variants, location, vaccination status, etc. Thus, these strategies can be, in theory, translated over to new variants in different regions of the world. Examples of robust feedback strategies for high disease transmission and a fixed testing capacity include (1) a single long lock down followed by a single long in-person period, and (2) multiple shorter lock downs followed by multiple shorter in-person periods. The utility of this approach of having multiple strategies is that administrators of universities, schools, business, etc. can use a strategy that is best adapted for their own functionality.

Ad Astra - telomeres in space!

PURPOSE: My journey to the stars began as I - along with the whole world - stood still and watched Neil Armstrong take those first small steps on the Moon. Fast forward 50 years and NASA astronauts Scott Kelly and Christina Koch each spend nearly a year in space aboard the International Space Station (ISS), a remarkable multinational collaborative project and floating U.S. National Laboratory that has supported continuous human presence in low Earth orbit for the past 20 years. Marking a new era of human space exploration, the first commercial rocket, SpaceX Falcon 9, recently launched NASA astronauts Doug Hurley and Bob Behnken in the Crew Dragon spacecraft Endeavor to the ISS and returned safely to Earth. NASA and its commercial partners are rapidly advancing innovative space technologies, and with the recently announced Artemis team of astronauts, plans to send the first woman and next man back to the moon and establish sustainable exploration by the end of the decade. Humankind will then be poised to take the next giant leap - pioneering human exploration of Mars. CONCLUSIONS: Historically, fewer than 600 individuals have participated in spaceflight, the vast majority of whom have been middle aged males (35-55 years) on short duration missions (less than 20 days). Thus, as the number and diversity of space travelers increase, a better understanding of how long-duration spaceflight affects human health is essential to maintaining individual astronaut performance during, and improving disease and aging trajectories following, future exploration missions. Here, I review findings from our NASA Twins Study and Telomeres investigations, highlighting potential mechanistic roles of chronic space radiation exposure in changes in telomere length and persistent DNA damage responses associated with long-duration spaceflight. Importantly, similar trends were observed in prostate cancer patients undergoing intensity-modulated radiation therapy (IMRT), additional support specifically for the role of radiation exposure. Individual differences in response were also observed in both cohorts, underscoring the importance of developing personalized approaches for evaluating human health effects and long-term outcomes associated with radiation exposures, whether on Earth or living in the extreme environment of space.

Renal Senescence, Telomere Shortening and Nitrosative Stress in Feline Chronic Kidney Disease.

Kidney tissues from cats with naturally occurring chronic kidney disease (CKD) and adult and senior cats without CKD were assessed to determine whether telomere shortening and nitrosative stress are associated with senescence in feline CKD. The histopathologic assessment of percent global glomerulosclerosis, inflammatory infiltrate, and fibrosis was performed. Senescence and nitrosative stress were evaluated utilizing p16 and iNOS immunohistochemistry, respectively. Renal telomere length was evaluated using telomere fluorescent in situ hybridization combined with immunohistochemistry. CKD cats were found to have significantly increased p16 staining in both the renal cortex and corticomedullary junction compared to adult and senior cats. Senior cats had significantly increased p16 staining in the corticomedullary junction compared to adult cats. p16 staining in both the renal cortex and corticomedullary junction were found to be significantly correlated with percent global glomerulosclerosis, cortical inflammatory infiltrate, and fibrosis scores. p16 staining also correlated with age in non-CKD cats. Average telomere length was significantly decreased in CKD cats compared to adult and senior cats. CKD cats had significantly increased iNOS staining compared to adult cats. Our results demonstrate increased renal senescence, telomere shortening, and nitrosative stress in feline CKD, identifying these patients as potential candidates for senolytic therapy with translational potential.

Climate change, activism, and supporting the mental health of children and young people: Perspectives from Western Australia.

The climate crisis has detrimental impacts on the mental health and wellbeing of children and young people. Psychological effects include feelings of fear, overwhelm, worry, distress, hopelessness and anger; PTSD; depression; anxiety; phobias; panic disorder; sleep disturbances; attachment disorders; learning difficulties; substance abuse; shock and trauma symptoms; adjustment problems; behavioural problems; and, suicidal thinking. First Nations' children and young people are particularly at risk due to loss of place, identity, culture, land and customs informed by kinship relationships with the Earth; while sustainable land use practices and connection to Country and community can enhance climate resilience. In Western Australia (WA), some young people engage in climate activism - including striking from school - to demand government action to address the causes of climate change, including colonisation and capitalism. Climate activism can promote resilience, particularly when children and young people can emotionally engage in the climate crisis; when mental health is systemically supported; when climate communication is transparent and comprehensive; and, when activism is informed by the knowledges and wisdoms of First Nations peoples and grounded on Country. This article is co-authored by WA young people, Aboriginal and non-Aboriginal academics, activists and practitioners engaged in youth, mental health and climate justice spaces. We argue for structural change to address the causes of the climate crisis, alongside enhanced evidence and approaches to appropriately support the mental health of children and young people. Furthermore, we support the call of Aboriginal peoples to ensure culturally appropriate, place-based responses based in caring for Country.

Destabilizing Effects of Ionizing Radiation on Chromosomes: Sizing up the Damage.

For long-term survival and evolution, all organisms have depended on a delicate balance between processes involved in maintaining stability of their genomes and opposing processes that lead toward destabilization. At the level of mammalian somatic cells in renewal tissues, events or conditions that can tip this balance toward instability have attracted special interest in connection with carcinogenesis. Mutations affecting DNA (and its subsequent repair) would, of course, be a major consideration here. These may occur spontaneously through endogenous cellular processes or as a result of exposure to mutagenic environmental agents. It is in this context that we discuss the rather unique destabilizing effects of ionizing radiation (IR) in terms of its ability to cause large-scale structural rearrangements to the genome. We present arguments supporting the conclusion that these and other important effects of IR originate largely from microscopically visible chromosome aberrations.

Haplotype diversity and sequence heterogeneity of human telomeres.

Telomeres are regions of repetitive nucleotide sequences capping the ends of eukaryotic chromosomes that protect against deterioration, and whose lengths can be correlated with age and adverse health risk factors. Yet, given their length and repetitive nature, telomeric regions are not easily reconstructed from short-read sequencing, thus making telomere sequencing, mapping, and variant resolution challenging problems. Recently, long-read sequencing, with read lengths measuring in hundreds of kilobase pairs, has made it possible to routinely read into telomeric regions and inspect their sequence structure. Here, we describe a framework for extracting telomeric reads from whole-genome single-molecule sequencing experiments, including de novo identification of telomere repeat motifs and repeat types, and also describe their sequence variation. We find that long, complex telomeric stretches and repeats can be accurately captured with long-read sequencing, observe extensive sequence heterogeneity of human telomeres, discover and localize noncanonical telomere sequence motifs (both previously reported, as well as novel), and validate them in short-read sequence data. These data reveal extensive intra- and inter-population diversity of repeats in telomeric haplotypes, reveal higher paternal inheritance of telomeric variants, and represent the first motif composition maps of multi-kilobase-pair human telomeric haplotypes across three distinct ancestries (Ashkenazi, Chinese, and Utah), which can aid in future studies of genetic variation, aging, and genome biology.

Effects of Synonymous Mutations beyond Codon Bias: The Evidence for Adaptive Synonymous Substitutions from Microbial Evolution Experiments.

Synonymous mutations are often assumed to be neutral with respect to fitness because they do not alter the encoded amino acid and so cannot be "seen" by natural selection. Yet a growing body of evidence suggests that synonymous mutations can have fitness effects that drive adaptive evolution through their impacts on gene expression and protein folding. Here, we review what microbial experiments have taught us about the contribution of synonymous mutations to adaptation. A survey of site-directed mutagenesis experiments reveals the distributions of fitness effects for nonsynonymous and synonymous mutations are more similar, especially for beneficial mutations, than expected if all synonymous mutations were neutral, suggesting they should drive adaptive evolution more often than is typically observed. A review of experimental evolution studies where synonymous mutations have contributed to adaptation shows they can impact fitness through a range of mechanisms including the creation of illicit RNA polymerase binding sites impacting transcription and changes to mRNA folding stability that modulate translation. We suggest that clonal interference in evolving microbial populations may be the reason synonymous mutations play a smaller role in adaptive evolution than expected based on their observed fitness effects. We finish by discussing the impacts of falsely assuming synonymous mutations are neutral and discuss directions for future work exploring the role of synonymous mutations in adaptive evolution.

Evaluation of DNA damage and stress in wildlife chronically exposed to low-dose, low-dose rate radiation from the Fukushima Dai-ichi Nuclear Power Plant accident.

The health effects associated with chronic low-dose, low-dose rate (LD-LDR) exposures to environmental radiation are uncertain. All dose-effect studies conducted outside controlled laboratory conditions are challenged by inherent complexities of ecological systems and difficulties quantifying dose to free-ranging organisms in natural environments. Consequently, the effects of chronic LD-LDR radiation exposures on wildlife health remain poorly understood and much debated. Here, samples from wild boar (Sus scrofa leucomystax) and rat snakes (Elaphe spp.) were collected between 2016 and 2018 across a gradient of radiation exposures in Fukushima, Japan. In vivo biomarkers of DNA damage and stress were evaluated as a function of multiple measurements of radiation dose. Specifically, we assessed frequencies of dicentric chromosomes (Telomere-Centromere Fluorescence in situ Hybridization: TC-FISH), telomere length (Telo-FISH, qPCR), and cortisol hormone levels (Enzyme Immunoassay: EIA) in wild boar, and telomere length (qPCR) in snakes. These biological parameters were then correlated to robust calculations of radiation dose rate at the time of capture and plausible upper bound lifetime dose, both of which incorporated internal and external dose. No significant relationships were observed between dicentric chromosome frequencies or telomere length and dose rate at capture or lifetime dose (p value range: 0.20-0.97). Radiation exposure significantly associated only with cortisol, where lower concentrations were associated with higher dose rates (r2 = 0.58; p < 0.0001), a relationship that was likely due to other (unmeasured) factors. Our results suggest that wild boar and snakes chronically exposed to LD-LDR radiation sufficient to prohibit human occupancy were not experiencing significant adverse health effects as assessed by biomarkers of DNA damage and stress.

Establishment of soil strength in a nourished wetland using thin layer placement of dredged sediment.

Coastal wetlands are experiencing accelerated rates of fragmentation and degradation due to sea-level rise, sediment deficits, subsidence, and salt-water intrusion. This reduces their ability to provide ecosystem benefits, such as wave attenuation, habitat for migratory birds, and a sink for carbon and nitrogen cycles. A deteriorated back barrier wetland in New Jersey, USA was nourished through thin layer placement (TLP) of dredged sediment in 2016. A field investigation was conducted in 2019 using a cone penetrometer (CPT) to quantify the establishment of soil strength post sediment nourishment compared to adjacent reference sites in conjunction with traditional wetland performance measures. Results show that the nourished area exhibited weaker strengths than the reference sites, suggesting the root system of the vegetation is still establishing. The belowground biomass measurements correlated to the CPT strength measurements, demonstrating that shear strength measured from the cone penetrometer could serve as a surrogate to monitor wetland vegetation trajectories. In addition, heavily trafficked areas underwent compaction from heavy equipment loads, inhibiting the development of vegetation and highlighting how sensitive wetlands are to anthropogenic disturbances. As the need for more expansive wetland restoration projects grow, the CPT can provide rapid high-resolution measurements across large areas supplying government and management agencies with vital establishment trajectories.

Telomere Length Dynamics and Chromosomal Instability for Predicting Individual Radiosensitivity and Risk via Machine Learning.

The ability to predict a cancer patient's response to radiotherapy and risk of developing adverse late health effects would greatly improve personalized treatment regimens and individual outcomes. Telomeres represent a compelling biomarker of individual radiosensitivity and risk, as exposure can result in dysfunctional telomere pathologies that coincidentally overlap with many radiation-induced late effects, ranging from degenerative conditions like fibrosis and cardiovascular disease to proliferative pathologies like cancer. Here, telomere length was longitudinally assessed in a cohort of fifteen prostate cancer patients undergoing Intensity Modulated Radiation Therapy (IMRT) utilizing Telomere Fluorescence in situ Hybridization (Telo-FISH). To evaluate genome instability and enhance predictions for individual patient risk of secondary malignancy, chromosome aberrations were assessed utilizing directional Genomic Hybridization (dGH) for high-resolution inversion detection. We present the first implementation of individual telomere length data in a machine learning model, XGBoost, trained on pre-radiotherapy (baseline) and in vitro exposed (4 Gy γ-rays) telomere length measurements, to predict post radiotherapy telomeric outcomes, which together with chromosomal instability provide insight into individual radiosensitivity and risk for radiation-induced late effects.