Publications by authors named "Christopher R Carey"

2 Publications

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Gene-nutrient interaction markedly influences yeast chronological lifespan.

Exp Gerontol 2016 12 25;86:113-123. Epub 2016 Apr 25.

Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA. Electronic address:

Purpose: Research into the genetic mechanisms of aging has expanded rapidly over the past two decades. This has in part been the result of the use of model organisms (particularly yeast, worms and flies) and high-throughput technologies, combined with a growing interest in aging research. Despite this progress, widespread consensus regarding the pathways that are fundamental to the modulation of cellular aging and lifespan for all organisms has been limited due to discrepancies between different studies. We have compared results from published genome-wide, chronological lifespan (CLS) screens of individual gene deletion strains in Saccharomyces cerevisiae in order to identify gene deletion strains with consistent influences on longevity as possible indicators of fundamental aging processes from this single-celled, eukaryotic model organism.

Methods: Three previous reports have described genetic modifiers of chronological aging in the budding yeast (S. cerevisiae) using the yeast gene deletion strain collection. We performed a comparison among the data sets using correlation and decile distribution analysis to describe concordance between screens and identify strains that consistently increased or decreased CLS. We used gene enrichment analysis in an effort to understand the biology underlying genes identified in multiple studies. We attempted to replicate the different experimental conditions employed by the screens to identify potential sources of variability in CLS worth further investigating.

Results: Among 3209 strains present in all three screens, nine deletions strains were in common in the longest-lived decile (2.80%) and thirteen were in common in the shortest-lived decile (4.05%) of all three screens. Similarly, pairwise overlap between screens was low. When the same comparison was extended to three deciles to include more mutants studied in common between the three screens, enrichment of cellular processes based on gene ontology analysis in the long-lived strains remained very limited. To test the hypothesis that different parental strain auxotrophic requirements or media formulations employed by the respective genome-wide screens might contribute to the lack of concordance, different CLS assay conditions were assessed in combination with strains having different ploidy and auxotrophic requirements (all relevant to differences in the way the three genome-wide CLS screens were performed). This limited but systematic analysis of CLS with respect to auxotrophy, ploidy, and media revealed several instances of gene-nutrient interaction.

Conclusions: There is surprisingly little overlap between the results of three independently performed genome-wide screens of CLS in S. cerevisiae. However, differences in strain genetic background (ploidy and specific auxotrophic requirements) were present, as well as different media and experimental conditions (e.g., aeration and pooled vs. individual culturing), which, along with stochastic effects such as genetic drift or selection of secondary mutations that suppress the loss of function from gene deletion, could in theory account for some of the lack of consensus between results. Considering the lack of overlap in CLS phenotypes among the set of genes reported by all three screens, and the results of a CLS experiment that systematically tested (incorporating extensive controls) for interactions between variables existing between the screens, we propose that discrepancies can be reconciled through deeper understanding of the influence of cell intrinsic factors such as auxotrophic requirements ploidy status, extrinsic factors such as media composition and aeration, as well as interactions that may occur between them, for example as a result of different pooling vs. individually aging cultures. Such factors may have a more significant impact on CLS outcomes than previously realized. Future studies that systematically account for these contextual factors, and can thus clarify the interactions between genetic and nutrient factors that alter CLS phenotypes, should aid more complete understanding of the underlying biology so that genetic principles of CLS in yeast can be extrapolated to differential cellular aging observed in animal models.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5079838PMC
http://dx.doi.org/10.1016/j.exger.2016.04.012DOI Listing
December 2016

Coupling to light, and transport and dissipation of energy in silver nanowires.

Phys Chem Chem Phys 2009 Jul 20;11(28):5889-96. Epub 2009 Apr 20.

Department of Chemistry, University of Notre Dame, Notre Dame, IN 46556-5670, USA.

Transient absorption experiments with diffraction-limited spatial resolution have been used to study the optical absorption properties and dynamics of isolated, single silver nanowires. The images and polarization analysis show that the near-IR pump and near-UV probe beams couple to fundamentally different electron motions. The near-IR pump laser excites the propagating surface plasmon polariton (SPP) modes of the wires when focused at the ends, and multipolar plasmon modes (antenna modes) for medial excitation. The images show that these two modes have comparable optical absorption cross-sections. In contrast, the near-UV probe couples to the transverse plasmon resonance of the wire independent of the spatial position. For either end-on or medial excitation, pump laser absorption causes lattice heating and coherently excites the breathing vibrational mode of the nanowires. The vibrational quality factors depend on the acoustic impedance mismatch between the nanowire and the environment, and are similar to those recently measured for silver nanocubes. Experiments performed with spatially separated pump and probe beams, with the pump beam focused at one end to excite the propagating SPP modes, show that the amplitudes of the initial transient absorption signal and the breathing motion decrease with distance along the wire. This arises because the propagating SPP mode decays as it moves down the wire, which reduces the number of electronic excitations and, therefore, the signal level in the experiments. The measured length scale for the SPP decay is similar to that obtained in previous light scattering experiments.
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http://dx.doi.org/10.1039/b901105fDOI Listing
July 2009