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578 results for “telomeres”
Data from: Primers to highly conserved elements optimized for qPCR-based telomere length measurements in vertebrates
<p>Telomere length dynamics are an established biomarker of health and aging in animals. The study of telomeres in numerous species has been facilitated by methods to measure telomere length by real-time quantitative PCR (qPCR). In this method, telomere length is determined by quantifying the amount of telomeric DNA repeats in a sample and normalizing this to the total amount of genomic DNA. This normalization requires the development of genomic reference primers suitable for qPCR, which remains challenging in non-model organism with genomes that have not been sequenced. Here we report reference primers that can be used in qPCR to measure telomere lengths in any vertebrate species. We designed primer pairs to amplify genetic elements that are highly conserved between evolutionarily distant taxa and tested them in species that span the vertebrate tree of life. We report five primer pairs that meet the specificity and reproducibility standards of qPCR. In addition, we demonstrate an approach to choose the best primers for a given species by testing the primers on multiple individuals within a species and then applying an established computational tool. These reference primers can facilitate qPCR-based telomere length measurements in any vertebrate species of ecological or economic interest.</p>
Data and code for 'Telomere length measurement for longitudinal analysis: the role of assay precision'
<p>Data and code for<strong> </strong>'Telomere length measurement for longitudinal analysis: implications of assay precision' by Nettle, Gadalla, Susser, Bateson and Aviv'</p> <p>The R script will run both the numerical simulations and the analysis of the empirical data. The exact results of the simulations will vary slightly from run to run.</p>
Biogeography of telomere dynamics in a vertebrate - Datasets S1
<p>Telomere length variation has been implicated in processes of ecological and evolutionary importance in a wide range of organisms. However, while the temporal component of this variation has been the subject of much research, we do not know yet whether a spatial component exists within species in telomere dynamics. Here, we investigated for the first time whether the biogeographic history of populations, a key driver of eco-evolutionary processes, can influence telomere dynamics. Based on a one-year longitudinal common-garden experiment in a tree frog species we found that co-specific populations can show striking differences in telomere dynamics, not explained by distinct environmental conditions experienced by individuals through time. Indeed, the populations did not differ in telomere length at the beginning of the study, yet they did after one year under standard conditions. We observed stability of telomere length over time within historically stable populations, but remarkable elongation (31.2% on average) within populations arisen during a recent range expansion. Our results suggest the intriguing scenario that non-equilibrium processes, such as range expansions, might promote plasticity in the molecular machinery regulating telomere dynamics.</p>
Data from: Telomere length reflects phenotypic quality and costs of reproduction in a long-lived seabird
Telomere length is associated with cellular senescence, lifestyle and ageing. Short telomeres indicate poor health in humans and reduced life expectancy in several bird species, but little is known about telomeres in relation to phenotypic quality in wild animals. We investigated telomere lengths in erythrocytes of known-age common terns (Sterna hirundo), a migratory seabird, in relation to arrival date and reproductive performance. Cross-sectional data revealed that, independent of age, individuals with short telomeres performed better: they arrived and reproduced earlier in the season and had more chicks in the nest. The latter effect was stronger the older the brood and stronger in males, which do most of the chick provisioning. Longitudinal data confirmed this pattern: compared with birds that lost their brood, birds that raised chicks beyond the 10th nestling day experienced higher telomere attrition from one year to the next. However, more detailed analysis revealed that the least and most successful individuals lost the fewest base pairs compared with birds with intermediate success. Our results suggest that reproductive success is achieved at the expense of telomeres, but that individual heterogeneity in susceptibility to such detrimental effects is important, as indicated by low telomere loss in the most successful birds.
Data from: How do growth and sibling competition affect telomere dynamics in the first month of life of long-lived seabird?
Telomeres are nucleotide sequences located at the ends of chromosomes that promote genome stability. Changes in telomere length (dynamics) are related to fitness or life expectancy, and telomere dynamics during the development phase are likely to be affected by growth and stress factors. Here, we examined telomere dynamics of black-tailed gull chicks (Larus crassirostris) in nests with and without siblings. We found that the initial telomere lengths of singletons at hatching were longer than those of siblings, indicating that singletons are higher-quality chicks than siblings in terms of telomere length. Other factors likely affecting individual quality (i.e., sex, laying date, laying order of eggs, and clutch size) were not related to telomere lengths. Within broods, initial telomere lengths were longer in older chicks than in younger chicks, suggesting that maternal effects, which vary with laying sequence, influence the initial lengths. Additionally, telomeres of chicks with a sibling showed more attrition between hatching and fledging than those of singleton chicks, suggesting that being raised with siblings can cause a sustained competitive environment that leads to telomere loss. High growth rates were associated with a low degree of telomere shortening observed in older siblings, perhaps because slower growth reflects higher food stress and/or higher aerobic metabolism from increased begging effort. Our results show that developmental telomere attrition was an inevitable consequence in two-chick nests in the pre- and post-hatching microenvironments due to the combination of social stress within the nest and maternal effects. The results of our study shed light on telomere dynamics in early life, which may represent an important physiological undercurrent of life-history traits.
Data from: Reduced telomere length in offspring of old fathers in a long-lived seabird
Evidence for transgenerational effects of senescence, whereby offspring from older parents have a reduced lifetime reproductive success, is increasing. Such effects could arise from compromised germline maintenance in old parents, potentially reflected in reduced telomere length in their offspring. We test the relationship between parental age and offspring early-life telomere length in a natural population of common terns and find a significant negative correlation between paternal age and offspring telomere length. Offspring telomere length is reduced by 35 base pairs for each additional year of paternal age. We find no correlation with maternal age. These results fit with the idea of compromised germline maintenance in males, whose germline stem cells require continued division.
Data from: Catching-up but telomere loss: half-opening the black box of growth and ageing trade-off in wild king penguin chicks
One of the reasons for animals not to grow as fast as they potentially could is that fast growth has been shown to be associated with reduced lifespan. However, we are still lacking a clear description of the reality of growth-dependent modulation of ageing mechanisms in wild animals. Using the particular growth trajectory of small king penguin chicks naturally exhibiting higher-than-normal growth rate to compensate for the winter break, we tested whether oxidative stress and telomere shortening are related to growth trajectories. Plasma antioxidant defences, oxidative damages levels and telomere length were measured at the beginning and the end of the post-winter growth period in three groups of chicks (small chicks which either passed away or survived the growth period, and large chicks). Small chicks that died early during the growth period had the highest level of oxidative damage and the shortest telomere lengths prior to death. Here, we show that small chicks that grew faster did it at the detriment of body maintenance mechanisms as shown by (i) higher oxidative damage and (ii) accelerated telomere loss. Our study provides the first evidence for a mechanistic link between growth and ageing rates under natural conditions.
Data from: Parallel telomere shortening in multiple body tissues owing to malaria infection
Several studies have shown associations between shorter telomere length in blood and weakened immune function, susceptibility to infections, and increased risk of morbidity and mortality. Recently, we have shown that malaria accelerates telomere attrition in blood cells and shortens lifespan in birds. However, the impact of infections on telomere attrition in different body tissues within an individual is unknown. Here, we tested whether malarial infection leads to parallel telomere shortening in blood and tissue samples from different organs. We experimentally infected siskins (Spinus spinus) with the avian malaria parasite Plasmodium ashfordi, and used real-time quantitative polymerase chain reaction (PCR) to measure telomere length in control and experimentally infected siskins. We found that experimentally infected birds showed faster telomere attrition in blood over the course of infection compared with control individuals (repeatedly measured over 105 days post-infection (DPI)). Shorter telomeres were also found in the tissue of all six major organs investigated (liver, lungs, spleen, heart, kidney, and brain) in infected birds compared with controls at 105 DPI. To the best of our knowledge, this is the first study showing that an infectious disease results in synchronous telomere shortening in the blood and tissue cells of internal organs within individuals, implying that the infection induces systemic stress. Our results have far-reaching implications for understanding how the short-term effects of an infection can translate into long-term costs, such as organ dysfunction, degenerative diseases, and ageing.
Data from: Shorter juvenile telomere length is associated with higher survival to spawning in migratory Atlantic salmon
The risk of mortality associated with a long-distance migration will depend on an animal's physiological state, as well as the prevailing ecological conditions. Here we assess whether juvenile telomere length, which in endotherms has been shown to be a biomarker of physiological state and expected lifespan, predicts whether wild Atlantic salmon Salmo salar successfully complete their marine migration. Over 1800 juvenile fish were trapped, measured, PIT-tagged and a tissue biopsy taken when migrating as juveniles down-river towards the sea. Survivors of the marine phase of the life cycle were then re-trapped and re-sampled when returning to the river to spawn as sexually mature adults, 1.5-2.5 years later. Most individuals experienced a reduction in telomere length during the marine migratory phase of their life cycle. While the relative rate of telomere loss was greater in males than females, telomere loss was unrelated to growth at sea. Contrary to expectations, salmon that had the shortest telomeres at the time of the outward migration had the greatest probability of surviving through to the return migration. This effect, independent of body size, may indicate a trade-off between investment in readiness for marine life (which favours high glucocorticoid levels, known to increase telomere attrition in other vertebrate species) and investment in telomere maintenance. Survival was also significantly influenced by the seasonal timing of outward migration, with the fish migrating downstream earliest in the spring having the highest probability of return. This study reveals that telomere length is associated with survival, although in ways that contrast with patterns seen in endotherms. This illustrates that while telomeres may be universally important for chromosome protection, the potential for telomere dynamics to predict performance may vary across taxa.
Data from: Early breeding females experience greater telomere loss
Annual reproductive success is often highest in individuals that initiate breeding early, yet relatively few individuals start breeding during this apparently optimal time. This suggests that individuals, particularly females who ultimately dictate when offspring are born, incur costs by initiating reproduction early in the season. We hypothesized that increases in the aging rate of somatic cells may be one such cost. Telomeres, the repetitive DNA sequences on the ends of chromosomes, may be good proxies of biological wear and tear as they shorten with age and in response to stress. Using historical data from a long-term study population of dark-eyed juncos (Junco hyemalis), we found that telomere loss between years was greater in earlier breeding females, regardless of chronological age. There was no relationship between telomere loss and the annual number of eggs laid or chicks that reached independence. However, telomere loss was greater when temperatures were cooler, and cooler temperatures generally occur early in the season. This suggests that environmental conditions could be the primary cause of accelerated telomere loss in early breeders.
Data from: Is telomere length a molecular marker of individual quality? insights from a long-lived bird
1. In wild vertebrates, some individuals survive and reproduce better than others and this has led to the concept of individual quality. Despite its importance when studying ecological processes and life-history trade-offs, measuring individual quality is complex because individuals must be followed during a large part of their life. 2. Recently, telomere biology has been successfully brought into ecology and telomere length has been suggested to be a promising molecular tool to evaluate individual quality in wild vertebrates ('the telomere – individual quality hypothesis'). 3. In this study, we tested this hypothesis in a long-lived species, the Black-browed albatross (Thalassarche melanophrys) by simultaneously measuring telomere length and several potential complementary phenotypic proxies of individual quality in a single year. In addition, we followed the return rate and the reproductive performance of these same albatrosses for a decade. 4. We found that long telomeres were associated with several markers of high individual quality (foraging behaviour, body size, and stress hormone levels). Furthermore, we found that a single measure of telomere length could predict future offspring productivity, for at least several years following telomere measurement (better productivity being associated with longer telomeres). 5. Altogether, these results support the 'telomere – individual quality hypothesis' and suggest that telomere length can be useful to estimate individual quality in long-lived seabirds.
Data from: Longitudinal evidence that older parents produce offspring with longer telomeres in a wild social bird
<p>As telomere length (TL) often predicts survival and lifespan, there is considerable interest in the origins of inter-individual variation in TL. Cross-generational effects of parental age on offspring TL are thought to be a key source of variation, but the rarity of longitudinal studies that examine the telomeres of successive offspring born throughout the lives of parents leaves such effects poorly understood. Here, we exploit TL measures of successive offspring produced throughout the long breeding tenures of parents in wild white-browed sparrow weaver (<i>Plocepasser mahali</i>) societies, to isolate the effects of within-parent changes in age on offspring TLs. Our analyses reveal the first evidence to date of a positive within-parent effect of advancing age on offspring TL: as individual parents age they produce offspring with longer telomeres (a modest effect that persists into offspring adulthood). We consider the potential for pre- and post-natal mechanisms to explain our findings. As telomere attrition predicts offspring survival to adulthood in this species, this positive parental age effect could impact parent and offspring fitness if it arose via differential telomere attrition during offspring development. Our findings support the view that cross-generational effects of parental age can be a source of inter-individual variation in TL.</p>
Supplementary material 5 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Table 5 : Data type: Table
Supplementary material 4 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Table 4 : Data type: Table
Supplementary material 1 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Table 1 : Data type: Table
Supplementary material 3 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Table 3 : Data type: Table
Supplementary material 7 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Figure 2 : Data type: Image
Supplementary material 2 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Table 2 : Data type: Table
Supplementary material 6 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Figure 1 : Data type: Image
Telomere-to-Telomere assembly and annotation of Prunus salicina 'Fengtangli'
<p>We generated a total of 26.84 Gb (~100× coverage, reads N50 of 17,471 bp) sequence coverage of raw PacBio high-fidelity long reads (HiFi) data and 30 Gb (∼120× coverage) of chromosome conformation capture sequencing (Hi-C) data for assembling the<em> Prunus</em> <em>salicina</em> ‘Fengtangli’ genome. For the initial assembly, the N50 value of contig-level for haplotype 1 and haplotype 2 were 20,111,805 bp and 19,658,610 bp, respectively, about 14 times that of the ‘Sanyueli’ contig-level assembly, with the largest contig reaching a length of 52,178,471bp. After anchoring and ordering, the scaffold N50 sizes reached 28.08 Mb and 28.37 Mb.24 of the expected 32 telomeres (8 chromosomes of two haplotypes) were identified, and 11 and 13 telomeres were found in PS_T2T_hap1 and PS_T2T_hap2.</p> <p>For gene annotation, 28,775 and 28,139 protein-coding genes were predicted for two haplotypes. BUSCOs assessment using the longest transcribed proteins revealed that two haplotypes captured 96.6% and 94.0% of a BUSCOs reference gene set, respectively.</p> <p>An Extensive de novo TE Annotator (EDTA) was used to generate a high-quality repetitive sequence library, and identified 119,630,196 bp and 121,705,710 bp of repetitive sequences in the two haplotypes, accounting for 45.41% and 46.19% of PS_T2T_hap1 and PS_T2T_hap2, respectively.</p>
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Allen Brain Atlas
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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