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1,683 results for “Senescence”
Effects of shading on tundra vegetation senescence at Toolik Lake, Coldfoot, Sagwon - Alaska 2016
Data on the effects of shading tundra vegetation from the sun when it is low in on the horizon in the north. If light quality was altered through shading, phenology might be affected. Senescence (color change) was measured for the common tundra species.
Eight Mile Lake Research Watershed, Carbon in Permafrost Experimental Heating Research (CiPEHR): Phenology of Dominant Plant Species I - Bud burst and Senescence 2013-2021
The Carbon in Permafrost Experimental Heating Research (CiPEHR) project addresses the following questions: 1) Does ecosystem warming cause a net release of C from the ecosystem to the atmosphere?, 2) Does the decomposition of old C, that comprises the bulk of the soil C pool, influence ecosystem C loss?, and 3) How do winter and summer warming alone, and in combination, affect ecosystem C exchange? We are answering these questions using a combination of field and laboratory experiments to measure ecosystem carbon balance and radiocarbon isotope ratios at a warming experiment located in an upland tundra field site near Healy, Alaska in the foothills of the Alaska Range. In this dataset we specifically ask, how does warming of soil and air impact the phenology of dominant plant species? Phenological data was collected to determine the timing of first bud break, onset and completion of senescence, and reproductive effort (flower and berry production).
Eight Mile Lake Research Watershed, Carbon in Permafrost Experimental Heating and Drying Research (DryPEHR): Phenology of Dominant Plant Species I - Bud burst and Senescence 2013-2021
This drying and warming experiment addresses the following questions: 1) Does ecosystem drying, warming and permafrost thaw cause a net release or uptake of C from the ecosystem to the atmosphere?, 2) Does the decomposition of old C that comprises the bulk of the soil C pool influence ecosystem C loss? 3) How do drying and warming affect plant communities and ecosystem properties? We are answering these questions using a combined warming and drying experiment (DryPEHR), which is situated with the Carbon in Permafrost Experimental Heating Research (CiPEHR) project and located in an upland tundra field site near Healy, Alaska in the foothills of the Alaska Range. Warming treatment here refers to growing season air temperature warming (~1C) using open top chambers (OTC) combined with soil 'warming' using snow fences during the snow covered months. Drying is achieved using an automated pumping system that lowers the water table in the dry plots. Soil warming began in 2008; OTCs and drying in 2011. In this dataset we specifically ask, how does warming and drying of soil and air impact the phenology of dominant plant species? Phenological data was collected to determine the timing of first bud break, onset and completion of senescence, and reproductive effort (flower and berry production).
Transcriptome analysis of the effect of over-expressing H2A.J mutants in proliferating WI38 fibroblasts for the paper entitled: The H2A.J histone variant contributes to Interferon-Stimulated Gene expression in senescence by its weak interaction with H1 and the derepression of repeated DNA sequences
<p>Abstract for overall study:</p> <p>The histone variant H2A.J was previously shown to accumulate in senescent human fibroblasts with persistent DNA damage to promote inflammatory gene expression, but its mechanism of action was unknown. We show that H2A.J accumulation contributes to weakening the association of histone H1 to chromatin and increasing its turnover. Decreased H1 in senescence is correlated with increased expression of some repeated DNA sequences, increased expression of STAT/IRF transcription factors, and transcriptional activation of Interferon-Stimulated Genes (ISGs). The H2A.J-specific Val-11 moderates the transcriptional activity of H2A.J, and H2A.J-specific Ser-123 can be phosphorylated in response to DNA damage with potentiation of its transcriptional activity by the phospho-mimetic S123E mutation. Our work demonstrates the functional importance of H2A.J-specific residues and potential mechanisms for its function in promoting inflammatory gene expression in senescence.</p> <p>Specific description for this dataset:</p> <p>H2A.J differs from canonical H2A only by a valine at position 11 instead of alanine, and the 7 C-terminal amino acids containing a potential minimal phosphorylation site SQ for DNA-damage response kinases. To test the functional importance of these H2A.J-specific sequences, we mutated Val-11 to Ala as is found in all canonical H2A sequences, and we mutated Ser-123 to either Glu to mimic a phospho-serine residue or to Ala to prevent phosphorylation. We also substituted the C-terminus of H2A.J with the C-terminus of H2A. These mutants, WT-H2A.J and canonical H2A-type1 were ectopically expressed in proliferating fibroblasts, and their microarray transcriptomes were compared to that of proliferating and senescent fibroblasts without ectopic histone expression. Genome-wide transcriptome analysis indicated that senescent fibroblasts clustered distinctly from proliferating fibroblasts, and proliferating fibroblasts expressing the H2A.J-V11A and H2A.J-S123E mutants clustered distinctly from fibroblasts expressing the other H2A.J mutants, WT-H2A.J, and H2A. Hallmark gene set enrichment analysis of the transcriptomes of fibroblasts expressing H2A.J-V11A or H2A.J-S123E versus control proliferating fibroblasts indicated that they showed the same highly significant enrichment for the Epithelial-Mesenchyme Transition, TNF-Alpha Signaling Via NF-kB, and Inflammatory Response gene sets. Notable inflammatory genes including IL1A, IL1B, IL6, CXCL8, and CCL2 are contained in these gene sets and are often induced in senescence as part of the senescence-associated secretory phenotype. Heat maps showed that the H2A.J-V11A and H2A.J-S123E mutants were particularly apt at activating the expression of these inflammatory genes in proliferating fibroblasts</p>
Supplementary material - Optical Diffraction Tomography and Raman Confocal Microscopy for the Investigation of Vacuoles Associated with Cancer Senescent Engulfing Cells
<p>Supplementary material containing the data used in the manuscript "Optical Diffraction Tomography and Raman Confocal Microscopy for the Investigation of Vacuoles Associated with Cancer Senescent Engulfing Cells"</p>
PhasAGE Expert Seminar- Inhibition of age-associated genomic instability: emerging strategy to delay cellular senescence and aging
<p>The PhasAGE <strong>Expert Seminars </strong>consist of a series of talks with speakers from PhasAGE partner’s institutions to promote a successful transfer of knowledge about PhasAGE topics – biomolecular phase separation, aging and age-related diseases.</p>
Decomposition of Microstegium vimineum litter, plants grew through the Big Oaks National Wildlife Refuge in 2019. Litter used in this experiment naturally senesced in the fall 2019, decomposition data collected through 2020. Plants were infected or not-infected with the foliar fungal pathogen Bipolaris gigantea during the 2019 growing season.
Decomposition of plant litter, facilitated primarily by microbial decomposers, plays a critical role in biogeochemical cycling and ecosystem function. Emerging pathogens have the potential to impact litter decomposition by altering the chemical composition and associated microbial community of host tissue. Here, we compared litter decomposition of the invasive grass Microstegium vimineum collected from sites with Bipolaris leaf spot symptoms and sites with no apparent disease symptoms in a common garden experiment. Our results revealed that leaf tissue from litter from non-infected sites decomposed more rapidly through the spring than litter from infected sites. Differences in fungal composition between infected and non-infected litter at the start of the experiment largely persisted through the summer. Our work demonstrates that pathogen colonization may facilitate the persistence of infected host litter, potentially slowing the return of nutrients to the environmental pool while also promoting the survival and dispersal of primary inoculum the following season.
Figure 4 in Aquatic Diptera (Insecta) assemblages in four sympatric Eryngium (Apiaceae) phytotelmata in flowering and senescent times
Figure 4. Median number of Metriocnemus eryngiotelmatus larvae per plant in four Eryngium phytotelmata. The box indicates the 25th and 75th centiles, the line within the box indicates the median and the whiskers indicate the 90th and 10th centiles. Different letters indicate significant differences detected by Dunn's test (p <0.05).
Figure 3 in Aquatic Diptera (Insecta) assemblages in four sympatric Eryngium (Apiaceae) phytotelmata in flowering and senescent times
Figure 3. Median number of Polypedilum parthenogeneticum larvae per plant in four Eryngium phytotelmata. The box indicates the 25th and 75th centiles, the line within the box indicates the median and the whiskers indicate the 90th and 10th centiles. Different letters indicate significant differences detected by Dunn's test (p <0.05).
Figure 2 in Aquatic Diptera (Insecta) assemblages in four sympatric Eryngium (Apiaceae) phytotelmata in flowering and senescent times
Figure 2. Cumulative total of Diptera observed in successive plants (n = 40 plants for each species in autumn and in spring). (A) Eryngium horridum; (B) Eryngium stenophyllum; (C) Eryngium aff. serra; (D) Eryngium elegans. Logarithmic equations with R2 values; p <0.001 for all R2 except for E. stenophyllum in autumn (p = 0.09).
Figure 2. Green and senescence N in Foliar resorption of nitrogen and phosphorus in Alcea apterocarpa (Malvaceae) in different habitats types
Figure 2. Green and senescence N:P ratio of A. apterocarpa in different habitat types. Means followed by the same letter are not significantly different at the 0.05 level using Tukey's HSD test.
Immunosuppression and senescence in dung beetles exposed to ivermectin
<p><span>Immunosuppression and premature senescence are main risks of exposure to toxic compounds that might define individual longevity and the fate of natural animal populations. However, these sublethal effects have not been studied in insects that are of fundamental importance for human economy and well-being such as dung beetles. We exposed adult dung beetles <em>Euoniticellus intermedius</em> to ivermectin, a commonly used antiparasitic drug in cattle that is excreted in dung, and measured immune activity through phenoloxidase (PO) and its zymogen, prophenoloxidase (proPO), in males and females of different ages. We predicted that both ivermectin exposure and age would reduce immune activity, with the negative effect of ivermectin being more pronounced in older individuals, revealing immunosenescence. Despite PO and proPO activities decreased with age and ivermectin exposure, ivermectin effects on these immune mechanisms were mainly constant across ages, revealing that immunosenescence is not an effect of ivermectin exposure. Whereas males suffered a reduction in PO and proPO with ivermectin and age, female proPO was not affected by ivermectin or age. This potentially reveals a strategy of self-care adopted by females to prioritize immune function when facing stressful conditions. Among sublethal effects caused by ivermectin in dung beetles, immunosuppression might be a main physiological driver of population declines in non-target beneficial fauna from contaminated environments.</span></p>
Modulation of fracture healing by the transient accumulation of senescent cells
<p>Senescent cells have detrimental effects across tissues with aging but may have beneficial effects on tissue repair, specifically on skin wound healing. However, the potential role of senescent cells in fracture healing has not been defined. Here, we performed an in silico analysis of public mRNAseq data and found that senescence and senescence-associated secretory phenotype (SASP) markers increased during fracture healing. We next directly established that the expression of senescence biomarkers increased markedly during murine fracture healing. We also identified cells in the fracture callus that displayed hallmarks of senescence, including distension of satellite heterochromatin and telomeric DNA damage; the specific identity of these cells, however, requires further characterization. Then, using a genetic mouse model (Cdkn2aLUC) containing a Cdkn2aInk4a-driven luciferase reporter, we demonstrated transient in vivo senescent cell accumulation during callus formation. Finally, we intermittently treated young adult mice following fracture with drugs that selectively eliminate senescent cells ('senolytics', Dasatinib plus Quercetin), and showed that this regimen both decreased senescence and SASP markers in the fracture callus and significantly accelerated the time course of fracture healing. Our findings thus demonstrate that senescent cells accumulate transiently in the murine fracture callus and, in contrast to the skin, their clearance does not impair but rather improves fracture healing.</p>
Data from: Pace and shape of senescence in three species of duckweed
<p>Senescence is progressive bodily deterioration associated with declines in survival and fecundity in older age classes. There is great diversity in patterns of senescence across species, but these patterns can be difficult to compare formally due to variation in the absolute time scales in which species live and die: members of some species live for a matter of days, others for millennia. To address this issue, the 'pace-shape' approach was developed to decouple absolute time from analyses and instead standardize life history traits in terms of average life expectancy, facilitating intra- and interspecific comparisons. Here, we use this approach to distinguish the generic form of demographic trajectories (shape) from the time scale on which the trajectories occurred (pace) in three species of tiny, free-floating aquatic plants known as duckweeds (<em>Lemna gibba</em> L., <em>L. minor</em> L., and <em>L. turionifera</em> Landolt), which have mean lifespans of less than a month under typical lab conditions, and exhibit age-related declines in survivorship and reproduction. Using a randomized block design in which we tracked a final total of 430 individuals, we report differences in pace and shape among the three species. Specifically, the largest, least-fecund, and typically longest-lived species, <em>L. gibba</em>, tended to exhibit more rapid decreases in time-standardized survivorship and fecundity compared to the other two species. This study emphasizes variation in aging patterns that can be found among plant species, including those in the same genus, and provides further validation for the utility of applying the pace and shape approach in interspecific comparisons.</p>
Life tables and graphs for Bahry (2022) - Equilibrium conditions in the evolution of senescence [MSc thesis, Carleton Univeristy]
<p>Life table data, and derived quantities, for <em>Equilibrium Conditions in the Evolution of Senescence</em> (Bahry, 2022, MSc thesis); adapted from the supplementary data of (Jones et al., 2014). Life table data for human (Japan 2009), human (Aché hunter-gatherer), fruit fly, Soay sheep, freshwater hydra, and desert tortoise.</p> <p>Basic life table quantities: age interval <span class="math-tex">\((X)\)</span>; survival function <span class="math-tex">\((l_X)\)</span>; and age-specific interval fecundity <span class="math-tex">\((m_X)\)</span>. Derived quantities include interval average force of mortality; reproductive value; residual reproductive value; Hamilton's indicators of the age-specific forces of selection; and actual age-specific mortality vs. predicted age-specific mortality based on models treated in (Bahry, 2022).</p> <p>In the original life tables of Jones et al. (2014), desert tortoises negatively senesce over the range of observed ages, but had a final observed cut-off age of 74; this causes reproductive value to artifactually fall to 0 as age-approached the cutoff. To get around this, I also used an extrapolated desert tortoise life table, assuming the age-74 mortality and fecundity rates remained constant until age 1000, then using the extrapolated life table to calculate reproductive value (and Hamilton's indicators) up to the cutoff age 74.</p> <p><strong>References</strong></p> <p>Bahry, D. (2022). <em>Equilibrium Conditions in the Evolution of Senescence</em> [Master's thesis, Carleton University].</p> <p>Jones, O. R. et al. (2014). Diversity of ageing across the tree of life. <em>Nature</em> 505: 169–174. https://doi.org/10.1038/nature12789</p>
Data from: Longitudinal gut microbiome dynamics in relation to age and senescence in a wild animal population
<p>In humans, gut microbiome (GM) differences are often correlated with, and sometimes causally implicated in, ageing. However, it is unclear how these findings translate in wild animal populations. Studies that investigate how GM dynamics change within individuals, and with declines in physiological condition, are needed to fully understand links between chronological age, senescence, and the GM, but have rarely been done. Here, we use longitudinal data collected from a closed population of Seychelles warblers (<em>Acrocephalus sechellensis</em>) to investigate how bacterial GM alpha diversity, composition, and stability are associated with host senescence. We hypothesised that GM diversity and composition will differ, and become more variable, in older adults, particularly in the terminal year prior to death, as the GM becomes increasingly dysregulated due to senescence. However, GM alpha diversity and composition remained largely invariable with respect to adult age and did not differ in an individual's terminal year. Furthermore, there was no evidence that the GM became more heterogenous in senescent age groups (individuals older than 6 years), or in the terminal year. Instead, environmental variables such as season, territory quality, and time of day, were the strongest predictors of GM variation in adult Seychelles warblers. These results contrast with studies on humans, captive animal populations, and some (but not all) studies on non-human primates, suggesting that GM deterioration may not be a universal hallmark of senescence in wild animal species. Further work is needed to disentangle the factors driving variation in GM-senescence relationships across different host taxa.</p>
Post-weaning survival in kangaroos is high and constant until senescence: Implications for population dynamics
<p>Large herbivores typically have consistently high prime-aged adult survival and lower, more variable, juvenile and senescent survival. Many kangaroo populations undergo greater fluctuations in density than other large herbivores, but age- and sex-specific survival of kangaroos and their response to environmental variation remain poorly estimated. We used long-term capture-mark-recapture data on 920 individuals to investigate the survival component of eastern grey kangaroo (<em>Macropus giganteus</em>) population dynamics. Forage availability and population density were monitored quarterly and included as predictors of survival in Bayesian Cormack-Jolly-Seber models. Annual survival probabilities were estimated for 5 age classes: 0 years (juveniles), 1–2 years (sub-adults), 3–6 years (prime-aged adults), 7–9 years (pre-senescent adults), and ≥10 years (senescent adults). Survival of juveniles varied widely during our 12-year study, ranging from 0.07–0.90 for females and 0.05–0.92 for males. Sub-adult survival was 0.80–0.93 for females and 0.75–0.85 for males, while that of prime-aged adults was ≥0.94 for females and ≥0.83 for males, despite large fluctuations in forage and density. The survival of pre-senescent adults spanned 0.86–0.93 for females and 0.60–0.86 for males. Senescent survival was variable, at 0.49–0.90 for females and 0.49–0.80 for males. Male survival was significantly lower than female survival in prime-aged and pre-senescent adults, but not in other age classes. Although most models supported by WAIC selection included one or a combination of environmental covariates, none of these individual covariates had a discernable effect on survival. Temporal variability in overall survival was mostly due to changes in survival of juvenile and senescent kangaroos. Kangaroo survival patterns are similar to those of ungulates, suggesting a strong role of sex-age structure on population dynamics.</p>
Data from: Reproductive senescence and mating tactic interact and conflict to drive reproductive success in a passerine
<p>An understanding of the drivers of individual fitness is a fundamental component of evolutionary ecology and life-history theory. Reproductive senescence, mate and mating tactic choice, and latent heterogeneity in individual quality interact to affect individual fitness. We sought to disentangle the effects of these fitness drivers, where longitudinal data are required to understand their respective impacts. We used reproductive allocation and success data from a long-term (1989-2018) study of white-throated dippers (Cinclus cinclus) in Switzerland to simultaneously examine the effects of female and male age, mating tactic, nest initiation date, and individual heterogeneity on reproductive performance. We modeled quadratic and categorical effects of age on reproductive parameters. The probability of polygyny increased with age in both sexes before declining in older age classes. Similarly, hatching probability in monogamous pairs and the number of nestlings hatched in both monogamous and polygynous pairs increased with female age before declining later in life. As predicted, offspring survival in monogamous pairs increased with male age before declining in older age classes, but male age had no effect on offspring survival in polygynous nesting attempts. Our results demonstrate that parental age, mating tactic, and individual heterogeneity all affect reproductive success, and that the impacts of senescent decline are expressed across different demographic components as a function of sex-specific senescent decline and mating tactic.</p>
Supplementary files to An integrated RNA-proteomic landscape of drug induced senescence in a cancer cell line.
<p>Senescent cells are characterized by an arrest in proliferation. In addition to replicative senescence resulting from telomere exhaustion, sub-lethal genotoxic stress resulting from DNA damage, oncogene activation, mitochondrial dysfunction or reactive metabolites also elicits a senescence phenotype. Senescence is a controlled programme affecting a wide variety of biological processes with some core hallmarks of senescence as well as tissue specific changes. This study presents an integrative multi-omic analysis of proteomic and RNA-seq from proliferating and senescent osteosarcoma cells. This study demonstrates senescence induction in a widely used cell line which can be used as a model system for characterising cancer cell responses to sub-lethal doses of chemotherapeutic agents, and makes available both RNA-seq and proteomic data from proliferating and senescent cells in open access repositories to aid reuse by the community.</p>
Supplementary material - Non-invasive Multimodal Imaging Reveals Early Therapy-Induced Senescence in Human Cancer Cells
<p>The repository features .xls and .txt worksheets including all the data used through this work and reported in the manuscript figures and graphs. More precisely, we included the following: </p> <ul> <li>Figure 2. Raw pixel-wise signals detected in NLO images of TIS cells control cells that were used to perform the colocalization graphs and analyses reported. We describe the average colocalization of SRS and F-CARS signals, and TPEF and E-CARS signals, in both phenotypes.</li> <li>Figure 4. Raw data from image analyses of TPEF and SRS channels of multimodal NLO images, divided in 5 different time points over the therapy follow-up period. The data describe the early rearrangement of mitochondria (TPEF) and lipid vesicles (SRS) in TIS cells, with respect to control counterparts.</li> <li>Figure 6. Raw data from image analyses of QPI images, divided in 4 different time points over the therapy follow-up period. The data describe the early morphological modifications of TIS cells, with respect to control counterparts.</li> </ul>
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