scholarly journals Accounting for phylogenetic relatedness in cross-species analyses of telomere shortening rates

2020 ◽  
Vol 1 ◽  
Author(s):  
Michael Le Pepke ◽  
Dan T.A. Eisenberg
Keyword(s):  
Multivariate Analysis ◽  
Body Mass ◽  
Dna Sequences ◽  
Phylogenetic Signal ◽  
Life History Strategies ◽  
Laboratory Mice ◽  
Telomere Shortening ◽  
Wild Mice ◽  
Phylogenetic Relatedness ◽  
Telomere Dynamics

AbstractTelomeres are repeating DNA sequences found on the ends of chromosomes, which shorten with age and are implicated in senescence. Cross-species analyses of telomere shortening rates (TSR) and telomere lengths are important for understanding mechanisms underlying senescence, lifespan and life-history strategies of different species. Whittemore et al. (2019) generated a new dataset on variation in TSR, lifespan and body mass. In phylogenetically uncorrected analyses they found that TSR negatively correlates with lifespan. We re-ran analyses of their dataset using appropriate phylogenetic corrections. We found a strong phylogenetic signal in the association between TSR and body mass. We were able to corroborate Whittemore et al.’s major findings, including while correcting for body mass in a multivariate analysis. Since laboratory mice have different telomere lengths and potentially different telomere dynamics than wild mice, we removed mice from the analysis, which attenuates most associations.

scholarly journals Polymorphism of Unique Noncoding DNA Sequences in Wild and Laboratory Mice

Genetics ◽  
1987 ◽  
Vol 117 (1) ◽  
pp. 101-108
Author(s):  
Felipe Figueroa ◽  
Masanori Kasahara ◽  
Herbert Tichy ◽  
Esther Neufeld ◽  
Uzi Ritte ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Inbred Mouse ◽  
Inbred Strains ◽  
Chromosome 17 ◽  
Mouse Strains ◽  
Laboratory Mice ◽  
Noncoding Dna ◽  
Wild Mice ◽  
Dna Library ◽  
T Complex

ABSTRACT Two DNA probes, D17Tul and D17Tu2, were isolated from a genomic DNA library containing only two mouse chromosomes, one of which is chromosome 17, carrying the major histocompatibility complex (H-2), as well as the t complex genes. The D17Tul probe was mapped to the centromeric region of chromosome 17 and the D17Tu2 probe to the S region of the H-2 complex. Neither of the two probes appeared to detect any genes, but both contained unique, nonrepetitive sequences. Typing of DNA obtained from a large panel of mice revealed the presence of four D17Tul patterns in inbred mouse strains, one very common, one less common, and two present in one strain each. The two common patterns could not be detected in appreciable frequencies in the European wild mice tested (one of the two patterns was, however, found in Australian wild mice). Conversely, the patterns found frequently in European wild mice are absent in the laboratory mice. We therefore conclude that wild mice from the sampled regions of Europe could not have provided the ancestral stocks from which inbred strains were derived. Only one D17Tul pattern was found in all the populations of Mus musculus tested, while eight patterns were found in Mus domesticus, with virtually all the populations being polymorphic. We suggest that this difference reflects different modes in which the two species colonized Europe. The distribution of the D17Tu2 patterns in inbred strains correlates with the distribution of H-2 haplotypes.

scholarly journals Natural variation in plant telomere length is associated with flowering time

2021 ◽  
Author(s):  
Jae Young Choi ◽  
Liliia R Abdulkina ◽  
Jun Yin ◽  
Inna B Chastukhina ◽  
John T Lovell ◽  
...  
Keyword(s):  
Life History ◽  
Telomere Length ◽  
Flowering Time ◽  
Dna Sequences ◽  
Genome Wide Association Study ◽  
Genomic Analysis ◽  
Life History Strategies ◽  
Length Variation ◽  
Chromosomal Structure ◽  
Chromosome Integrity

Abstract Telomeres are highly repetitive DNA sequences found at the ends of chromosomes that protect the chromosomes from deterioration during cell division. Here, using whole genome re-sequencing and terminal restriction fragment assays, we found substantial natural intraspecific variation in telomere length in Arabidopsis thaliana, rice (Oryza sativa), and maize (Zea mays). Genome-wide association study (GWAS) mapping in A. thaliana identified 13 regions with GWAS-significant associations underlying telomere length variation, including a region that harbors the telomerase reverse transcriptase (TERT) gene. Population genomic analysis provided evidence for a selective sweep at the TERT region associated with longer telomeres. We found that telomere length is negatively correlated with flowering time variation not only in A. thaliana, but also in maize and rice, indicating a link between life history traits and chromosome integrity. Our results point to several possible reasons for this correlation, including the possibility that longer telomeres may be more adaptive in plants that have faster developmental rates (and therefore flower earlier). Our work suggests that chromosomal structure itself might be an adaptive trait associated with plant life history strategies.

Multivariate analysis of quantitative trait loci influencing variation in anxiety-related behavior in laboratory mice

2004 ◽  
Vol 15 (2) ◽  
pp. 69-76 ◽  
Author(s):  
Maria Grazia Turri ◽  
John C. DeFries ◽  
Norman D. Henderson ◽  
Jonathan Flint
Keyword(s):  
Multivariate Analysis ◽  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Laboratory Mice ◽  
Trait Loci

scholarly journals Risk Assessment for Use of a Porcine Circovirus-Contaminated Reagent in a Barrier Maintained Rodent Colony

2020 ◽  
Vol 59 (5) ◽  
pp. 575-579
Author(s):  
Norman C Peterson ◽  
Aaron A Berlin
Keyword(s):  
Risk Assessment ◽  
Mouse Model ◽  
Cell Cultures ◽  
Direct Contact ◽  
Model Development ◽  
Porcine Circovirus ◽  
Laboratory Mice ◽  
Wild Mice ◽  
Pancreatic Elastase ◽  
Porcine Pancreatic Elastase

A proposal for the use of porcine pancreatic elastase (PPE) to develop a mouse model of pulmonary emphysema raised concerns about introducing contaminating porcine viruses into our barrier facility. Porcine Circovirus (PCV) is a known contaminant of vaccines and cell cultures that have been exposed to porcine-derived reagents. Endemic infection of PCV3 in laboratory mice has been reported, and some evidence supports natural PCV infection in wild mice. PPE samples from 2 different vendors tested positive for DNA from both PCV2 and 3. To allow model development with these reagents to proceed, we developed a protocol that would meet scientific objectives, minimize exposure of mice, and provide information on the potential for the virus to spread. Five d after BALB/c mice received intralaryngeal administration of PPE, lungs were harvested and analyzed for evidence of disease. Tissues from other major organs were submitted to test for disseminated PCV2 and 3 DNA. Similarly, tissues (including lungs) from direct contact nude sentinel mice were analyzed for the presence of the virus. To evaluate the possibility of endemic PCV2/3 infection, we also surveyed non-porcine reagent exposed mice on other studies. PCV2 and 3 was not detected in any of the tissues submitted. Although this study provided no evidence of infection and transmission of PCV2/3 from the contaminated PPE sample over the 5 d study, further work is needed to understand the risks and impact of introducing PCV contaminated cells or reagents into barrier maintained rodent colonies.

scholarly journals Evolutionary heritage influences Amazon tree ecology

2016 ◽  
Vol 283 (1844) ◽  
pp. 20161587 ◽  
Author(s):  
Fernanda Coelho de Souza ◽  
Kyle G. Dexter ◽  
Oliver L. Phillips ◽  
Roel J. W. Brienen ◽  
Jerome Chave ◽  
...  
Keyword(s):  
Life History ◽  
Evolutionary History ◽  
Large Scale ◽  
Phylogenetic Signal ◽  
Life History Strategies ◽  
Relative Importance ◽  
Life History Variation ◽  
Trait Variation ◽  
Closed Canopy ◽  
Repeated Evolution

Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change.

scholarly journals Thogoto Virus Lacking Interferon-Antagonistic Protein ML Is Strongly Attenuated in Newborn Mx1-Positive but Not Mx1-Negative Mice

2004 ◽  
Vol 78 (20) ◽  
pp. 11422-11424 ◽  
Author(s):  
Andreas Pichlmair ◽  
Johanna Buse ◽  
Stephanie Jennings ◽  
Otto Haller ◽  
Georg Kochs ◽  
...  
Keyword(s):  
Animal Models ◽  
Standard Laboratory ◽  
Laboratory Mice ◽  
Highly Pathogenic ◽  
Wild Mice ◽  
Effector Molecules ◽  
Conventional Animal ◽  
Infected Cells ◽  
Virus Mutant ◽  
Interferon Antagonists

ABSTRACT The Thogoto virus ML protein suppresses interferon synthesis in infected cells. Nevertheless, a virus mutant lacking ML remained highly pathogenic in standard laboratory mice. It was strongly attenuated, however, in mice carrying the interferon-responsive Mx1 gene found in wild mice, demonstrating that enhanced interferon synthesis is protective only if appropriate antiviral effector molecules are present. Our study shows that the virulence-enhancing effects of some viral interferon antagonists may escape detection in conventional animal models.

A multivariate analysis of variation in genome size and endoreduplication in angiosperms reveals strong phylogenetic signal and association with phenotypic traits

2012 ◽  
Vol 196 (4) ◽  
pp. 1240-1250 ◽  
Author(s):  
Jillian D. Bainard ◽  
Luke D. Bainard ◽  
Thomas A. Henry ◽  
Aron J. Fazekas ◽  
Steven G. Newmaster
Keyword(s):  
Multivariate Analysis ◽  
Genome Size ◽  
Phylogenetic Signal ◽  
Phenotypic Traits ◽  
Analysis Of Variation

Association Between Body Mass Index and Perioperative Mortality After Repair of Ruptured Abdominal Aortic Aneurysms

2020 ◽  
Vol 54 (7) ◽  
pp. 573-578
Author(s):  
Tiffany W. Liang ◽  
S. Keisin Wang ◽  
Paul D. Dimusto ◽  
Christopher M. McAninch ◽  
Charles W. Acher ◽  
...  
Keyword(s):  
Body Mass Index ◽  
Multivariate Analysis ◽  
Body Mass ◽  
Mortality Risk ◽  
Significant Risk ◽  
Abdominal Aortic Aneurysms ◽  
Aortic Aneurysms ◽  
Perioperative Mortality ◽  
Abdominal Aortic ◽  
Ruptured Abdominal Aortic Aneurysms

Objective: The attempt to repair a ruptured abdominal aortic aneurysm carries a significant risk of perioperative mortality. The relationship between body mass index (BMI) and outcomes after repair of ruptured abdominal aortic aneurysms (AAAs) has not been well defined. We report the association of BMI with outcomes after ruptured AAA repair. Methods: Patients undergoing ruptured AAA repairs between 2008 and 2017 at 2 tertiary academic centers were included in this retrospective study. Demographics (including BMI), type of repair, length of stay, and admission mortality risk scores were gathered and analyzed using bivariate and multivariate logistic regressions. Adjusted odds ratio (AOR) was reported with 95% CIs and P values from the multivariate analysis. The primary outcome was 30-day mortality. Akaike information criterion (AIC) and c-statistics were used to assess the predictive power of models including physiologic score with or without BMI. Results: A total of 202 patients underwent repair of ruptured AAA. In bivariate relationship, increased BMI was significantly associated with 30-day mortality. With multivariate analysis, adjusting for demographics, type of procedure, and physiologic score, for each kg/m2 increase in BMI, an 8% increase in the likelihood of perioperative mortality (AOR = 1.08, 95% CI: 1.01-1.17; P = .04) was observed. Conclusion: When adjusted for admission risk score, type of procedure, and demographics, obesity was associated with increased 30-day mortality. With BMI as an additional data point, the c-statistics and AIC comparisons indicated that we would have a greater ability to preoperatively estimate mortality after ruptured AAA repair. Consideration could be made to include BMI in future mortality risk scoring systems for ruptured AAA.

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