Measuring telomere length and telomere dynamics in evolutionary biology and ecology.
Ontology highlight
ABSTRACT:
SUBMITTER: Nussey DH
PROVIDER: S-EPMC4375921 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Telomere length dynamics plays a crucial role in regulation of cellular processes and cell fate. In contrast to epidemiological studies revealing the association of telomere length with age, age-related diseases, and cancers, the role of telomeres in regulation of transcriptome and epigenome and the role of genomic variations in telomere lengthening are not extensively analyzed. This is explained by the fact that experimental assays for telomere length measurement are resource consuming, and there are very few studies where high-throughput genomics, transcriptomics, and/or epigenomics experiments have been coupled with telomere length measurements. Recent development of computational approaches for assessment of telomere length from whole genome sequencing data pave a new perspective on integration of telomeres into high-throughput systems biology analysis framework. Herein, we review existing methodologies for telomere length measurement and compare them to computational approaches, as well as discuss their applications in large-scale studies on telomere length dynamics.
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Project description:Individual chromosome arms have specific individual telomere lengths (TLs). Past studies within species have shown strong positive correlations between individual chromosome length and TL at that chromosome. While the reasons for these associations are unclear, the strength and consistency of the associations across disparate taxa suggest that this is important to telomere biology and should be explored further. If TL is primarily determined by chromosome length, then chromosome length should be considered and controlled for in cross-species analyses of TL. Here, we employ a cross-species approach to explore whether the chromosome length-TL association observed intraspecifically is a determinant of mean TL across species. Data were compiled from two studies characterizing TL across a range of mammalian taxa and analysed in a phylogenetic framework. We found no significant relationship between TL and chromosome size across mammals or within mammalians orders. The pattern trends in the expected direction and we suggest may be masked by evolutionary lag effects.
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Project description:Telomeres cap chromosome ends and are critical for genomic stability. Many telomere-associated proteins are important for telomere length maintenance. Recent genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) in genes encoding telomere-associated proteins (RTEL1 and TERT-CLPTM1) as markers of cancer risk. We conducted an association study of telomere length and 743 SNPs in 43 telomere biology genes. Telomere length in peripheral blood DNA was determined by Q-PCR in 3,646 participants from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial and Nurses' Health Study. We investigated associations by SNP, gene, and pathway (functional group). We found no associations between telomere length and SNPs in TERT-CLPTM1L or RTEL1. Telomere length was not significantly associated with specific functional groups. Thirteen SNPs from four genes (MEN1, MRE11A, RECQL5, and TNKS) were significantly associated with telomere length. The strongest findings were in MEN1 (gene-based P=0.006), menin, which associates with the telomerase promoter and may negatively regulate telomerase. This large association study did not find strong associations with telomere length. The combination of limited diversity and evolutionary conservation suggest that these genes may be under selective pressure. More work is needed to explore the role of genetic variants in telomere length regulation.
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Project description:Osteosarcoma, the most common primary bone tumor, occurs most frequently in adolescents. Chromosomal aneuploidy is common in osteosarcoma cells, suggesting underlying chromosomal instability. Telomeres, located at chromosome ends, are essential for genomic stability; several studies have suggested that germline telomere length (TL) is associated with cancer risk. We hypothesized that TL and/or common genetic variation in telomere biology genes may be associated with risk of osteosarcoma. We investigated TL in peripheral blood DNA and 713 single nucleotide polymorphisms (SNPs) from 39 telomere biology genes in 98 osteosarcoma cases and 69 orthopedic controls. For the genotyping component, we added 1363 controls from the Prostate, Lung, Colorectal, and Ovarian Cancer ScreeningTrial. Short TL was not associated with osteosarcoma risk overall (OR 1.39, P=0.67), although there was a statistically significant association in females (OR 4.35, 95% Cl 1.20-15.74, P=0.03). Genotype analyses identified seven SNPs in TERF1 significantly associated with osteosarcoma risk after Bonferroni correction by gene. These SNPs were highly linked and associated with a reduced risk of osteosarcoma (OR 0.48-0.53, P=0.0001-0.0006). We also investigated associations between TL and telomere gene SNPs in osteosarcoma cases and orthopedic controls. Several SNPs were associated with TL prior to Bonferroni correction; one SNP in NOLA2 and one in MEN1 were marginally non-significant after correction (P(adj)=0.057 and 0.066, respectively). This pilot-study suggests that females with short telomeres may be at increased risk of osteosarcoma, and that SNPs in TERF1 are inversely associated with osteosarcoma risk.
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Project description:Telomeres represent the nucleotide repeat sequences at the ends of chromosomes and are essential for chromosome stability. They can shorten at each round of DNA replication mainly because of incomplete DNA synthesis of the lagging strand. Reduced relative telomere length is associated with aging and a range of disease states. Different methods such as terminal restriction fragment analysis, real-time quantitative PCR (qPCR) and fluorescence in situ hybridization are available to measure telomere length; however, the qPCR-based method is commonly used for large population-based studies. There are multiple variations across qPCR-based methods, including the choice of the single-copy gene, primer sequences, reagents, and data analysis methods in the different reported studies so far. Here, we provide a detailed step-by-step protocol that we have optimized and successfully tested in the hands of other users. This protocol will help researchers interested in measuring relative telomere lengths in cells or across larger clinical cohort/study samples to determine associations of telomere length with health and disease.
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Project description:Disparities remain in the representation of marginalized students in STEM. Classroom-based experiential learning opportunities can increase student confidence and academic success; however, the effectiveness of extending learning to outdoor settings is unknown. Our objectives were to examine (a) demographic gaps in ecology and evolutionary biology (EEB) major completion, college graduation, and GPAs for students who did and did not enroll in field courses, (b) whether under-represented demographic groups were less likely to enroll in field courses, and (c) whether under-represented demographic groups were more likely to feel increased competency in science-related tasks (hereafter, self-efficacy) after participating in field courses. We compared the relationships among academic success measures and demographic data (race/ethnicity, socioeconomic status, first-generation, and gender) for UC Santa Cruz undergraduate students admitted between 2008 and 2019 who participated in field courses (N = 941 students) and who did not (N = 28,215 students). Additionally, we administered longitudinal surveys to evaluate self-efficacy gains during field-based versus classroom-based courses (N = 570 students). We found no differences in the proportion of students matriculating at the university as undecided, proposed EEB, or proposed other majors across demographic groups. However, five years later, under-represented students were significantly less likely to graduate with EEB degrees, indicating retention rather than recruitment drives disparities in representation. This retention gap is partly due to a lower rate of college completion and partly through attrition to other majors. Although under-represented students were less likely to enroll in field courses, field courses were associated with higher self-efficacy gains, higher college graduation rates, higher EEB major retention, and higher GPAs at graduation. All demographic groups experienced significant increases in self-efficacy during field-based but not lecture-based courses. Together, our findings suggest that increasing the number of field courses and actively facilitating access to students from under-represented groups can be a powerful tool for increasing STEM diversity.
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Project description:The integration of theory and data drives progress in science, but a persistent barrier to such integration in ecology and evolutionary biology is that theory is often developed and expressed in the form of mathematical models that can feel daunting and inaccessible for students and empiricists with variable quantitative training and attitudes towards math. A promising way to make mathematical models more approachable is to embed them into interactive tools with which one can visually evaluate model structures and directly explore model outcomes through simulation. To promote such interactive learning of quantitative models, we developed EcoEvoApps, a collection of free, open-source, and multilingual R/Shiny apps that include model overviews, interactive model simulations, and code to implement these models directly in R. The package currently focuses on canonical models of population dynamics, species interactions, and landscape ecology. These apps help illustrate fundamental results from theoretical ecology and can serve as valuable teaching tools in classroom settings. We present data from student surveys which show that students rate these apps as useful learning tools, and that using interactive apps leads to substantial gains in students' interest and confidence in working with mathematical models. This points to the potential for interactive activities to make theoretical models more accessible to a wider audience, and thus facilitate the feedback between theory and data across ecology and evolutionary biology.
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Project description:Average telomere length (TL) in blood cells has been shown to decline with age in a range of vertebrate species, and there is evidence that TL is a heritable trait associated with late-life health and mortality in humans. In non-human mammals, few studies to date have examined lifelong telomere dynamics and no study has estimated the heritability of TL, despite these being important steps towards assessing the potential of TL as a biomarker of productive lifespan and health in livestock species. Here we measured relative leukocyte TL (RLTL) in 1,328 samples from 308 Holstein Friesian dairy cows and in 284 samples from 38 female calves. We found that RLTL declines after birth but remains relatively stable in adult life. We also calculated the first heritability estimates of RLTL in a livestock species which were 0.38 (SE = 0.03) and 0.32 (SE = 0.08) for the cow and the calf dataset, respectively. RLTL measured at the ages of one and five years were positively correlated with productive lifespan (p < 0.05). We conclude that bovine RLTL is a heritable trait, and its association with productive lifespan may be used in breeding programmes aiming to enhance cow longevity.
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Project description:Fabry disease (FD) leads to significant morbidity and mortality, which may indicate accelerated ageing. However, it is still unclear whether there is a relationship between telomere length (TL), a marker of biological ageing, and disease outcome. We aimed to examine the relationship between leukocyte TL (LTL) dynamics and the presence of advanced disease stages and/or late complications of FD, including hypertrophic cardiomyopathy, nephropathy and stroke, both cross-sectionally and longitudinally. DNA was extracted from peripheral blood leukocytes and quantitative PCR was utilized to determine relative LTL in 99 Fabry patients. In the longitudinal analysis, we included 50 patients in whom at least three measurements were performed over a period of 5-10 years. The results showed a significant inverse correlation between LTL and age (ρ = -0.20, p = 0.05). No significant differences in LTL were found between females and males (p = 0.79) or between patients receiving disease-specific therapy and those without (p = 0.34). In a cross-sectional analysis, no association was found between the presence (p = 0.15) or number (p = 0.28) of advanced stages of the disease and/or late complications and LTL. Similarly, in a longitudinal analysis, no difference in LTL dynamics was found regarding the presence (p = 0.16) of advanced stage organ involvement and/or late complications or their number. These findings indicate that LTL dynamics in adulthood may not be a reliable indicator of disease outcomes in Fabry patients. Therefore, LTL may more accurately reflect the disease burden in early life, when TL is primarily determined.
| S-EPMC11351930 | biostudies-literature
Project description:BackgroundTelomere length (TL) is considered a biological marker of aging and may indicate age-related disease susceptibility. Adults and children show a fixed ranking and tracking of TL over time. However, the contribution of an individual's initial birth TL to their later life TL is unknown. We evaluated change and tracking of TL from birth to child- and adulthood.MethodsTelomere length at birth was measured using qPCR in two independent prospective birth cohorts. After a median follow-up period of 4 years in ENVIRONAGE (n = 273) we assessed leukocyte telomere length (LTL) and after 23 years in EFPTS (n = 164) buccal TL was assessed. Correlations and multivariable regression models were applied to study telomere tracking and determinants of TL change from birth onwards.FindingsIn children, LTL at the age of 4 correlates with TL at the start of life both in cord blood (r = 0.71, P < 0.0001;) and placenta (r = 0.60, P < 0.0001) and was -11.2% and -33.1% shorter, respectively. In adulthood, buccal TL at the age of 23 correlates with placental TL (r = 0.46, P < 0.0001) and was -35.9% shorter. TL attrition was higher in individuals with longer birth TL. However, based on TL ranking, individuals do not tend to change dramatically from TL rank after 4 or 23 years of follow-up. Finally, longer maternal TL associates with lower telomere attrition in the next generation.InterpretationThe high prediction of newborn TL for later life TL, and stable TL ranking from birth onwards underscores the importance of understanding the initial setting of newborn TL and its significance for later life.FundingEuropean Research Council (ERC-StG310898) and Flemish Scientific Fund (12X9620N).
| S-EPMC7808927 | biostudies-literature