Shortest-Path Network Analysis Is a Useful Approach toward Identifying Genetic Determinants of Longevity

Background

Identification of genes that modulate longevity is a major focus of aging-related research and an area of intense public interest. In addition to facilitating an improved understanding of the basic mechanisms of aging, such genes represent potential targets for therapeutic intervention in multiple age-associated diseases, including cancer, heart disease, diabetes, and neurodegenerative disorders. To date, however, targeted efforts at identifying longevity-associated genes have been limited by a lack of predictive power, and useful algorithms for candidate gene-identification have also been lacking.

Methodology/Principal Findings

We have utilized a shortest-path network analysis to identify novel genes that modulate longevity in Saccharomyces cerevisiae. Based on a set of previously reported genes associated with increased life span, we applied a shortest-path network algorithm to a pre-existing protein–protein interaction dataset in order to construct a shortest-path longevity network. To validate this network, the replicative aging potential of 88 single-gene deletion strains corresponding to predicted components of the shortest-path longevity network was determined. Here we report that the single-gene deletion strains identified by our shortest-path longevity analysis are significantly enriched for mutations conferring either increased or decreased replicative life span, relative to a randomly selected set of 564 single-gene deletion strains or to the current data set available for the entire haploid deletion collection. Further, we report the identification of previously unknown longevity genes, several of which function in a conserved longevity pathway believed to mediate life span extension in response to dietary restriction.

Conclusions/Significance

This work demonstrates that shortest-path network analysis is a useful approach toward identifying genetic determinants of longevity and represents the first application of network analysis of aging to be extensively validated in a biological system. The novel longevity genes identified in this study are likely to yield further insight into the molecular mechanisms of aging and age-associated disease.     

“How” and “Why” prompts in forensic investigative interviews with preschool children

Although young children may frequently be asked “How” and “Why” questions, it is unclear whether they have the ability to respond well enough to justify the use of these words during investigative interviews. The range of possible uses and interpretations of the words “How” and “Why” makes it critical to examine their use when communicatively immature children are interviewed. In this study, police interviews of 3- to 5-year-old suspected victims of sexual abuse (n = 49) were examined. The use of How/Why prompts by interviewers and children’s responses to interviewers’ How/Why prompts were coded. How/Why prompts represented 22% of all interviewer prompts. Of all details provided by children, however, 8.5% were in response to How/Why prompts. In addition, children provided the information sought in response to only 20% of the interviewers’ How/Why prompts, whereas uninformative responses were relatively common. Children responded to more How/Why prompts with the information sought by interviewers as they grew older. The findings suggest that How/Why prompts may not be particularly effective when interviewing preschool children.     

Feeding responses to particle-bound cues by a deposit-feeding spionid polychaete, Dipolydora quadrilobata (Jacobi 1883)

In marine soft-sediment habitats, chemical sensing by deposit-feeding organisms most likely plays a critical role in feeding behavior, yet, few specifics about this role and its ecological implications are known. We show that several particle-bound chemical cues stimulate feeding activity of a spionid polychaete Dipolydora quadrilobata (Jacobi 1883). Using glass beads as a proxy for sediment, we tested for feeding responses to a selected number of potential cues that might be used to indicate food availability or quality. We presented two sets of beads to individual intact worms: one with and one without covalently bound compounds such as single amino acids, mixtures of amino acids, and single simple sugars. Worms were exposed to the beads under slow flowing seawater so that any dissolved cues were flushed from the test chamber. Each worm was videotaped for 15 min immediately following the addition of beads, and these records were scored for the time the worm spent in a variety of behaviors. Responses to beads with and without cues were compared to identify compounds as stimulatory, inhibitory, or inactive. Five of the seven particle-bound cues tested significantly increased feeding activity, and none of those tested were found to be inhibitory.     

Host‐parasitoid dynamics in periodic boreal moths

We analyse the population and spatial structures of coastal annual-plant communities, across ten dunes and three years, to explore the role of seed mass in structuring these communities. One suggestion is that annual-plant communities are structured by competition-colonization trade-offs driven by difference among species in seed-allocation strategies, while another perspective is that seed mass influences the ways in which species respond to environmental variation. In support of the competition-colonization trade-off, the two largest-seeded species found on the dunes ( Erodium cicutarium and Geranium molle ) were negatively associated with the other guild members at the 10-mm scale in 1995, suggesting they locally excluded smaller-seeded species in that year (when population densities were high). In support of the environmental response hypothesis, populations of annual plants declined between 1995 and 1996 on eight of the ten dunes, underscoring the importance of year-to-year environmental fluctuations in determining population sizes. The species that became relatively uncommon also became more aggregated in space, and this effect was most pronounced among the small-seeded species. Thus, small-seeded species may be forced to retreat into refuges when conditions are unfavourable, where reduced frequencies of interspecific contacts may increase their chances of persistence. We also show that small-seeded species sometimes reach much higher population densities than larger-seeded species, consistent with earlier findings, but reason that this abundance/seed mass relationship could have resulted from either a competition-colonization trade-off or from different responses of small- and large-seeded species to environmental variation. We conclude that dune-annual species with contrasting seed masses respond differently to environmental variation, while the competition-colonization trade-off plays a lesser role in community dynamics than previously considered.     

Functional analysis of a frame-shift mutant of the dihydropyridine receptor pore subunit (α1S) expressing two complementary protein fragments

Background  

The L-type Ca²⁺ channel formed by the dihydropyridine receptor (DHPR) of skeletal muscle senses the membrane voltage and opens the ryanodine receptor (RyR1). This channel-to-channel coupling is essential for Ca²⁺ signaling but poorly understood. We characterized a single-base frame-shift mutant of α_1S, the pore subunit of the DHPR, that has the unusual ability to function voltage sensor for excitation-contraction (EC) coupling by virtue of expressing two complementary hemi-Ca²⁺ channel fragments.     

Stepping stone speciation in Hawaii’s flycatchers: molecular divergence supports new island endemics within the elepaio

The elepaio (Chasiempis sandwichensis) is a monarch flycatcher endemic to the Hawaiian Islands of Kauai, Oahu, and Hawaii. Elepaio vary in morphology among and within islands, and five subspecies are currently recognized. We investigated phylogeography of elepaio using mitochondrial (ND2) and nuclear (LDH) markers and population structure within Hawaii using ND2 and microsatellites. Phylogenetic analyses revealed elepaio on each island formed reciprocally monophyletic groups, with Kauai ancestral to other elepaio. Sequence divergence in ND2 among islands (3.02–2.21%) was similar to that in other avian sibling species. Estimation of divergence times using relaxed molecular clock models indicated elepaio colonized Kauai 2.33 million years ago (95% CI 0.92–3.87 myr), Oahu 0.69 (0.29–1.19) myr ago, and Hawaii 0.49 (0.21–0.84) myr ago. LDH showed less variation than ND2 and was not phylogenetically informative. Analysis of molecular variance within Hawaii showed structure at ND2 (fixation index = 0.31), but microsatellites showed no population structure. Genetic, morphological, and behavioral evidence supports splitting elepaio into three species, one on each island, but does not support recognition of subspecies within Hawaii or other islands. Morphological variation in elepaio has evolved at small geographic scales within islands due to short dispersal distances and steep climatic gradients. Divergence has been limited by lack of dispersal barriers in the extensive forest that once covered each island, but anthropogenic habitat fragmentation and declines in elepaio population size are likely to decrease gene flow and accelerate differentiation, especially on Oahu.     

Quantifying shape and ecology in avian pedal claws: The relationship between the bony core and keratinous sheath

Terrestrial tetrapods use their claws to interact with their environments in a plethora of ways. Birds in particular have developed a diversity of claw shapes since they are often not bound to terrestrial locomotion and have heterogeneous body masses ranging several orders of magnitude. Numerous previous studies have hypothesized a connection between pedal claw shape and ecological mode in birds, yet have generated conflicting results, spanning from clear ecological groupings based on claw shape to a complete overlap of ecological modes. The majority of these studies have relied on traditional morphometric arc measurements of keratinous sheaths and have variably accounted for likely confounding factors such as body mass and phylogenetic relatedness. To better address the hypothesized relationship between ecology and claw shape in birds, we collected 580 radiographs allowing visualization of the bony core and keratinous sheath shape in 21 avian orders. Geometric morphometrics was used to quantify bony core and keratinous sheath shape and was compared to results using traditional arc measurements. Neither approach significantly separates bird claws into coarse ecological categories after integrating body size and phylogenetic relatedness; however, some separation between ecological groups is evident and we find a gradual shift from the claw shape of ground‐dwelling birds to those of predatory birds. Further, the bony claw core and keratinous sheath are significantly correlated, and the degree of functional integration does not differ across ecological groups. Therefore, it is likely possible to compare fossil bony cores with extant keratinous sheaths after applying corrections. Finally, traditional metrics and geometric morphometric shape are significantly, yet loosely correlated. Based on these results, future workers are encouraged to use geometric morphometric approaches to study claw geometry and account for confounding factors such as body size, phylogeny, and individual variation prior to predicting ecology in fossil taxa.     

On the oxidation of alkyl and aryl sulfides by [(Me3TACN)MnO(OH)2]: A density functional study

Density functional theory suggests that the formal 2-electron oxidation of sulfides, RR′S, to sulfoxides, by the model Mn^VO catalyst, [(TACN)Mn^V O(OH)₂]⁺, proceeds in two quite distinct 1-electron steps. Transfer of the first electron is barrierless and generates a sulfur radical cation, antiferromagnetically coupled to a Mn^IV centre via a covalent μ-oxo bridge. The second electron-transfer step is accompanied by migration of the oxygen atom to the sulfur centre, and is rate-determining. The absence of a barrier in the first step, where a sulfur radical is formed, means that the presence of electron-donating or withdrawing substituents on the sulfide has only a minor impact on the rate of reaction.     

Evolution of coding and non-coding genes in HOX clusters of a marsupial

ABSTRACT: BACKGROUND: The HOX gene clusters are thought to be highly conserved amongst mammals and othervertebrates, but the long non-coding RNAs have only been studied in detail in human andmouse. The sequencing of the kangaroo genome provides an opportunity to use comparativeanalyses to compare the HOX clusters of a mammal with a distinct body plan to those ofother mammals. RESULTS: Here we report a comparative analysis of HOX gene clusters between an Australian marsupialof the kangaroo family and the eutherians. There was a strikingly high level of conservationof HOX gene sequence and structure and non-protein coding genes including the microRNAsmiRNA-196a, miRNA-196b, miRNA-10a and miRNA-10b and the long non-coding RNAsHOTAIR, HOTAIRM1 and HOXA11AS that play critical roles in regulating gene expressionand controlling development. By microRNA deep sequencing and comparative genomicanalyses, two conserved microRNAs (miR-10a and miR-10b) were identified and one newcandidate microRNA with typical hairpin precursor structure that is expressed in bothfibroblasts and testes was found. The prediction of microRNA target analysis showed thatseveral known microRNA targets, such as mir-10, mir-414 and mir-464, were found in thetammar HOX clusters. In addition, several novel and putative miRNAs were identified thatoriginated from elsewhere in the tammar genome and that target the tammar HOXB andHOXD clusters. CONCLUSIONS: This study confirms that the emergence of known long non-coding RNAs in the HOXclusters clearly predate the marsupial-eutherian divergence 160 Ma ago. It also identified anew potentially functional microRNA as well as conserved miRNAs. These non-codingRNAs may participate in the regulation of HOX genes to influence the body plan of thismarsupial.