Algorithms

Publication Title: 
Mechanisms of Ageing and Development

Accessible and readily utilized software, tables and approximation formulae have been developed to estimate power and sample size for studies of time to event (survival times) when the survival times are assumed to be exponential. These methods can markedly misestimate power when the distribution is Weibull and not exponential. The Weibull distribution with increasing hazard is common in aging research, especially when the whole life span of the subjects is of interest.

Author(s): 
Heo, M.
Faith, M. S.
Allison, D. B.
Publication Title: 
BMC bioinformatics

BACKGROUND: Differential coexpression is a change in coexpression between genes that may reflect 'rewiring' of transcriptional networks. It has previously been hypothesized that such changes might be occurring over time in the lifespan of an organism. While both coexpression and differential expression of genes have been previously studied in life stage change or aging, differential coexpression has not. Generalizing differential coexpression analysis to many time points presents a methodological challenge.

Author(s): 
Gillis, Jesse
Pavlidis, Paul
Publication Title: 
Fly

Understanding the causes of aging is a complex problem due to the multiple factors that influence aging, which include genetics, environment, metabolism and reproduction, among others. These multiple factors create logistical difficulties in the evaluation of anti-aging agents. There is a need for good model systems to evaluate potential anti-aging compounds.

Author(s): 
Jafari, Mahtab
Publication Title: 
Cell Cycle (Georgetown, Tex.)

Macroautophagy is a self-cannibalistic process that enables cells to adapt to various stresses and maintain energy homeostasis. Additionally, autophagy is an important route for turnover of misfolded proteins and damaged organelles, with important implications in cancer, neurodegenerative diseases and aging. Resveratrol and spermidine are able to induce autophagy by affecting deacetylases and acetylases, respectively, and have been found to extend the life-span of model organisms.

Author(s): 
Bennetzen, Martin V.
MariÒo, Guillermo
Pultz, Dennis
Morselli, Eugenia
FÊrgeman, Nils J.
Kroemer, Guido
Andersen, Jens S.
Publication Title: 
The Journals of Gerontology. Series A, Biological Sciences and Medical Sciences

Comparative studies of aging are often difficult to interpret because of the different factors that tend to correlate with longevity. We used the AnAge database to study these factors, particularly metabolism and developmental schedules, previously associated with longevity in vertebrate species. Our results show that, after correcting for body mass and phylogeny, basal metabolic rate does not correlate with longevity in eutherians or birds, although it negatively correlates with marsupial longevity and time to maturity.

Author(s): 
de Magalh„es, Jo„o Pedro
Costa, Joana
Church, George M.
Publication Title: 
Biology Letters

Resveratrol has shown evidence of decreasing cancer incidence, heart disease, metabolic syndrome and neural degeneration in animal studies. However, the effects on longevity are mixed. We aimed to quantify the current knowledge of life extension from resveratrol. We used meta-analytic techniques to assess the effect resveratrol has on survival, using data from 19 published papers, including six species: yeast, nematodes, mice, fruitflies, Mexican fruitflies and turquoise killifish. Overall, our results indicate that resveratrol acts as a life-extending agent.

Author(s): 
Hector, Katie L.
Lagisz, Malgorzata
Nakagawa, Shinichi
Publication Title: 
Nature Communications

The growing availability of 'omics' data and high-quality in silico genome-scale metabolic models (GSMMs) provide a golden opportunity for the systematic identification of new metabolic drug targets. Extant GSMM-based methods aim at identifying drug targets that would kill the target cell, focusing on antibiotics or cancer treatments. However, normal human metabolism is altered in many diseases and the therapeutic goal is fundamentally different--to retrieve the healthy state. Here we present a generic metabolic transformation algorithm (MTA) addressing this issue.

Author(s): 
Yizhak, Keren
Gabay, Orshay
Cohen, Haim
Ruppin, Eytan
Publication Title: 
The Journal of Biological Chemistry

At the core of Saccharomyces cerevisiae telomeres is an array of tandem telomeric DNA repeats bound site-specifically by multiple Rap1 molecules. There, Rap1 orchestrates the binding of additional telomere-associated proteins and negatively regulates both telomere fusion and length homeostasis. Using electron microscopy, viscosity, and light scattering measurements, we show that purified Rap1 is a monomer in solution that adopts a ringlike or C shape with a central cavity.

Author(s): 
Williams, Tanya L.
Levy, Daniel L.
Maki-Yonekura, Saori
Yonekura, Koji
Blackburn, Elizabeth H.
Publication Title: 
PloS One

BACKGROUND: Premature shortening of leukocyte telomere length has been proposed as a novel mechanism by which depression may confer increased risk of adverse cardiovascular events. Prior studies demonstrating associations of depression and depressive symptoms with shorter leukocyte telomere length were small, included selected psychiatric outpatients, were based on convenience samples, and/or adjusted for a limited number of possible confounding factors.

Author(s): 
Shaffer, Jonathan A.
Epel, Elissa
Kang, Min Suk
Ye, Siqin
Schwartz, Joseph E.
Davidson, Karina W.
Kirkland, Susan
Honig, Lawrence S.
Shimbo, Daichi
Publication Title: 
BMC bioinformatics

BACKGROUND: CpG islands (CGIs), clusters of CpG dinucleotides in GC-rich regions, are often located in the 5' end of genes and considered gene markers. Hackenberg et al. (2006) recently developed a new algorithm, CpGcluster, which uses a completely different mathematical approach from previous traditional algorithms. Their evaluation suggests that CpGcluster provides a much more efficient approach to detecting functional clusters or islands of CpGs. RESULTS: We systematically compared CpGcluster with the traditional algorithm by Takai and Jones (2002).

Author(s): 
Han, Leng
Zhao, Zhongming

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