The molecular scaffold kinase suppressor of Ras 1 is a modifier of RasV12-induced and replicative senescence

In primary mouse embryo fibroblasts (MEFs), oncogenic Ras induces growth arrest via Raf/MEK/extracellular signal-regulated kinase (ERK)-mediated activation of the p19ARF/p53 and INK4/Rb tumor suppressor pathways. Ablation of these same pathways causes spontaneous immortalization in MEFs, and oncogenic transformation by Ras requires ablation of one or both of these pathways. We show that Kinase Suppressor of Ras 1 (KSR1), a molecular scaffold for the Raf/MEK/ERK cascade, is necessary for RasV12-induced senescence, and its disruption enhances primary MEF immortalization. RasV12 failed to induce p53, p19ARF, p16INK4a, and p15INK4b expression in KSR1-/- MEFs and increased proliferation instead of causing growth arrest. Reintroduction of wild-type KSR1, but not a mutated KSR1 construct unable to bind activated ERK, rescued RasV12-induced senescence. On continuous culture, deletion of KSR1 accelerated the establishment of spontaneously immortalized cultures and increased the proportion of cultures escaping replicative crisis. Despite enhancing escape from both RasV12-induced and replicative senescence, however, both primary and immortalized KSR1-/- MEFs are completely resistant to RasV12-induced transformation. These data show that escape from senescence is not necessarily a precursor for oncogenic transformation. Furthermore, these data indicate that KSR1 is a member of a unique class of proteins whose deletion blocks both senescence and transformation.     

Structural variation and evolution of a defense-gene cluster in natural populations of Aegilops tauschii

Genetic mapping and sequencing of plant genomes have been useful for investigating eukaryotic chromosome structural organization. In many cases, analyses have been limited in the number of representatives sampled from specific groups. The degree of intraspecific genome diversity remains in question. The possibility exists that a single model genome may have limited utility for identifying genes in related members of the species or genus. Crop improvement programs have particular interests in disease resistance genes that are harbored by wild relatives of modern cultivated crops. These genes are evolutionarily dynamic and under selective pressure by a broad range of pathogenic organisms. Using resistance gene analogs as models for gene evolution, intraspecific genome comparisons were made among populations of wild diploid wheat (Aegilops tauschii). We observed that deletion haplotypes are occurring frequently and independently in the genome. Haplotypes are geographically correlated and maintenance of gene complements in localized populations indicates selective advantage. Furthermore, deletion haplotypes are not detrimental to plant health, since genes without adaptive value in alternate environments are eliminated from the genome. Deletion haplotypes appear to be a common form of allelic variation in plants, and we address the consequences on genome restructuring and gene evolution. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Genomic signatures to guide the use of chemotherapeutics

Using in vitro drug sensitivity data coupled with Affymetrix microarray data, we developed gene expression signatures that predict sensitivity to individual chemotherapeutic drugs. Each signature was validated with response data from an independent set of cell line studies. We further show that many of these signatures can accurately predict clinical response in individuals treated with these drugs. Notably, signatures developed to predict response to individual agents, when combined, could also predict response to multidrug regimens. Finally, we integrated the chemotherapy response signatures with signatures of oncogenic pathway deregulation to identify new therapeutic strategies that make use of all available drugs. The development of gene expression profiles that can predict response to commonly used cytotoxic agents provides opportunities to better use these drugs, including using them in combination with existing targeted therapies.     

Epistatic analysis of the roles of the RAD27 and POL4 gene products in DNA base excision repair in S. cerevisiae

The cellular role of the DNA polymerase encoded by the Saccharomyces cerevisiae POL4 gene is unclear. We have used an epistasis analysis to investigate whether the proteins encoded by the POL4 and RAD27 genes participate in alternative, non-redundant subpathways of DNA base excision repair (BER). We constructed strains in which the genes were deleted singly or in combination and have examined their sensitivity to DNA damaging agents as well as spontaneous mutation frequency. The double deletion strain is no more sensitive to damaging agents and has no higher spontaneous mutation frequency than the most sensitive single mutant. These data indicate that the protein encoded by the POL4 gene does not participate in a non-redundant subpathway of base excision repair under these conditions. We discuss the implications of these results in light of the recent classification of the POL4 gene product as a member of the DNA polymerase lambda family.     

Histidine pK(a) values for the N-lobe of human transferrin: effect of substitution of binding site Asp by Ser (D63S)

The pK(a) values have been determined for eight of the nine histidine residues and the amino terminus of the N-lobe of human apo-transferrin (hTF/2N), and for seven of the nine histidine residues and the amino terminus of the protein Asp63Ser hTF/2N containing a mutation of the Fe(3+)-ligand Asp63 to Ser63. Calculations suggested that substitution of aspartate by serine would result in decreases of the pK(a) values of most of the histidine residues in the protein. This was found to be the case experimentally, and allowed assignment of the varepsilonCH resonance of His249. For the wild-type protein, the His residue with a pK(a) of 7.40 was assigned as His249, whereas for the mutant, no observable His residue had a pK(a) value higher than 6.9. The protonated form of His249 appears to be stabilised by interactions with Asp63, and the high pK(a) value may be critical for ensuring the release of iron at endosomal pH (5.5). The mutation lowered the apparent binding constant of hTF/2N for the synergistic anion oxalate from log K 4.0 to log K 3.3. (1)H NMR spectral changes induced by Ga(3+) binding to the mutant are compared to those observed for the wild-type protein.     

Hand-Rearing and Sex Determination Tool for the Taveta Golden Weaver (Ploceus castaneiceps)

Improvements in the ability to hand‐rear birds in captivity have aided zoological institutions in the sustainable management of these species, and have provided opportunities to examine their physical growth in varying conditions. Monitoring the weight gain and development of chicks is an important aspect of developing a hand‐rearing protocol. In this paper we provide the institutional history for a colonial species of passerine, the Taveta golden weaver, at Disney's Animal Kingdom®, in order to demonstrate the methods of establishing a successful breeding program which largely incorporates hand‐rearing in management of the population. We also tested if we could accurately predict sex of chicks using weights collected on Day 14 during the hand‐rearing process. Using this tool, we were able to correctly determine sex before fledging in more than 83% of chicks. Early sex determination is important in captive species for genetic management and husbandry purposes. While genetic sexing can be expensive, we found that using growth curves to determine sex can be a reliable and cost‐effective tool for population management of a colonial passerine. Zoo Biol. 31:600‐608, 2012. © 2012 Wiley Periodicals, Inc.     

The diversity of aging models

Most of the signalling pathways involved in aging regulation have been recently found well conserved at various levels throughout the evolution. Taking this into account, a diversity of model organisms, including worms, rodents, and lemurs as well, allows to address different questions: how to understand the interactions between genetic and environmental factors while challenging theories of aging, to preserve hearing integrity, to fight against senescence of neural stem cells, or to explore brain fitness from gene expression to cognitive and social behavior? Here are the main issues that can be considered, stressing the complementarities of the models. The differentiation of aging physiological aspects from those induced by age-related pathologies will also be specified. By emphasizing recent ability of technologies to promote new aging insights, we discuss towards a better understanding of mechanisms governing aging.     

Steller sea lion spatial‐use patterns derived from a Bayesian model of opportunistic observations

Despite acquisition of a substantial catalog of telemetry data from Steller sea lions (Eumetopias jubatus) over the past two decades, scientists still lack comprehensive regionally explicit knowledge about Steller sea lion habitat use. The Platforms of Opportunity data contain records of Steller sea lion sightings throughout the species’ entire range and have potential to fill gaps in knowledge about their spatial use; however, the data have not previously been used because effort (e.g., time spent surveying or area sampled) was not recorded when sightings were obtained. For this study a novel approach was used to overcome the lack of effort data through development of an effort index and a Bayesian negative binomial model. The model quantified Steller sea lion encounter rates and associated uncertainty within 15 × 15 km² grid cells across the species’ entire range. Year‐round, as well as breeding and nonbreeding season encounter rates were estimated. The results of this analysis identify several previously undocumented areas of high use by Steller sea lions, indicate that only 37% of Steller sea lion high‐use areas fall within designated critical habitat, and demonstrate that use of depth and distance from shore as indicators of Steller sea lion habitat is contraindicated.