Dual function of Rpn5 in two PCI complexes, the 26S proteasome and COP9 signalosome

Subunit composition and architectural structure of the 26S proteasome lid is strictly conserved between all eukaryotes. This eight-subunit complex bears high similarity to the eukaryotic translation initiation factor 3 and to the COP9 signalosome (CSN), which together define the proteasome CSN/COP9/initiation factor (PCI) troika. In some unicellular eukaryotes, the latter two complexes lack key subunits, encouraging questions about the conservation of their structural design. Here we demonstrate that, in Saccharomyces cerevisiae, Rpn5 plays dual roles by stabilizing proteasome and CSN structures independently. Proteasome and CSN complexes are easily dissected, with Rpn5 the only subunit in common. Together with Rpn5, we identified a total of six bona fide subunits at roughly stoichiometric ratios in isolated, affinity-purified CSN. Moreover, the copy of Rpn5 associated with the CSN is required for enzymatic hydrolysis of Rub1/Nedd8 conjugated to cullins. We propose that multitasking by a single subunit, Rpn5 in this case, allows it to function in different complexes simultaneously. These observations demonstrate that functional substitution of subunits by paralogues is feasible, implying that the canonical composition of the three PCI complexes in S. cerevisiae is more robust than hitherto appreciated.     

Contributions to the faunistics and bionomics of Staphylinidae (Coleoptera) in northeastern North America: discoveries made through study of the University of Guelph Insect Collection, Ontario, Canada

Staphylinidae (Rove Beetles) from northeastern North America deposited in the University of Guelph Insect Collection (Ontario, Canada) were curated from 2008-2010 by the first author. The identification of this material has resulted in the recognition of thirty-five new provincial or state records, six new Canadian records, one new record for the United States and two new records for eastern Canada. All records are for subfamilies other than Aleocharinae and Pselaphinae, which will be treated in future publications as collaborative projects. Range expansions of ten exotic species to additional provinces and states are reported. The known distributions of each species in northeastern North America are summarized and presented as maps, and those species with a distinctive habitus are illustrated with color photographs. Genitalia and/or secondary sexual characters are illustrated for those species currently only identifiable on the basis of dissected males. The majority of the new records are in groups that have been recently revised, demonstrating the importance of curation and local insect surveys to the understanding of biodiversity, even for taxa and areas considered 'relatively well-known'.     

The impact of habitat fragmentation on trophic interactions of the monophagous butterfly <Emphasis Type="Italic">Polyommatus coridon</Emphasis>

Theory predicts that habitat fragmentation, including reduced area and connectivity of suitable habitat, changes multitrophic interactions. Species at the bottom of trophic cascades (host plants) are expected to be less negatively affected than higher trophic levels, such as herbivores and their parasitoids or predators. Here we test this hypothesis regarding the effects of habitat area and connectivity in a trophic system with three levels: first with the population size of the larval food plant Hippocrepis comosa, next with the population density of the monophagous butterfly species Polyommatus coridon and finally with its larval parasitism rate. Our results show no evidence for negative effects of habitat fragmentation on the food plant or on parasitism rates, but population density of adult P. coridon was reduced with decreasing connectivity. We conclude that the highly specialized butterfly species is more affected by habitat fragmentation than its larval food plant because of its higher trophic position. However, the butterfly host species was also more affected than its parasitoids, presumably because of lower resource specialization of local parasitoids which also frequently occur in alternative hosts. Therefore, conservation efforts should focus first on the most specialized species of interaction networks and second on higher trophic levels.     

Infestation of the invasive mollusc <Emphasis Type="Italic">Crepidula fornicata</Emphasis> by the native shell borer <Emphasis Type="Italic">Cliona celata</Emphasis>: a case of high parasite load without detrimental effects

The temporal prevalence of the widespread boring sponge Cliona celata and its effects were analysed in a population of the invasive mollusc Crepidula fornicata. This mollusc produces extra shell material when infested with the endolithic sponge, suggesting that infestation may be detrimental for C. fornicata growth and/or reproduction. For 37 months, size, sex, female reproductive status and sponge-infestation stage were recorded for 300 individuals sampled every month in the Bay of Morlaix (France). In the 12,049 individuals examined, the prevalence of C. celata was high with a monthly average of 43.1% of the individuals hosting the sponge. The relative proportion of heavily infested individuals generally increased over time. Nevertheless, a cyclic decrease occurred every 10 months, suggesting putative episodes of mortality of heavily infested individuals. The gregarious behaviour of the mollusc seemed to promote the high prevalence of the sponge, which may propagate through contact between neighbouring C. fornicata individuals. Due to the sex-size relationship in protandrous C. fornicata, females were far more infested than males. We did not find evidence for a cost of producing extra shell material on somatic growth or on female fertility, and the boring sponge is unlikely to substantially affect the sex-change patterns in C. fornicata. The limited effects of the endolithic sponge on C. fornicata contrasts with the documented damage to some local species, including commercially exploited shellfish, suggesting that C. fornicata may alter the infestation dynamics in the surrounding native community. Dedicated studies are now needed to investigate the extent and mechanisms of these species interactions.     

Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires

Background  

Genome size and complexity, as measured by the number of genes or protein domains, is remarkably similar in most extant eukaryotes and generally exhibits no correlation with their morphological complexity. Underlying trends in the evolution of the functional content and capabilities of different eukaryotic genomes might be hidden by simultaneous gains and losses of genes.     

Toward rational design of bacterial genomes

The advent of genetic engineering-the ability to edit and insert DNA into living organisms-in the latter half of the 20th century created visions of a new era of synthetic biology, where novel biological functions could be designed and implemented for useful purposes. We are witnessing an exciting revolution of scale, wherein technical progresses allow for the manipulation of genetic material at the whole genome level. This will enable the manufacture of increasingly complex genetic designs to solve pressing challenges in health, energy and the environment-if and when such designs can be specified. We argue that the organized development of key common application organisms, engineered for engineerability, and attendant libraries of parts, pathways and standardized manufacturing are necessary for this genome-scale technology to realize its promise.     

An Investigation of the Effects of Sports-related Concussion in Youth Using Functional Magnetic Resonance Imaging and the Head Impact Telemetry System

One of the most commonly reported injuries in children who participate in sports is concussion or mild traumatic brain injury (mTBI)¹. Children and youth involved in organized sports such as competitive hockey are nearly six times more likely to suffer a severe concussion compared to children involved in other leisure physical activities². While the most common cognitive sequelae of mTBI appear similar for children and adults, the recovery profile and breadth of consequences in children remains largely unknown², as does the influence of pre-injury characteristics (e.g. gender) and injury details (e.g. magnitude and direction of impact) on long-term outcomes. Competitive sports, such as hockey, allow the rare opportunity to utilize a pre-post design to obtain pre-injury data before concussion occurs on youth characteristics and functioning and to relate this to outcome following injury. Our primary goals are to refine pediatric concussion diagnosis and management based on research evidence that is specific to children and youth. To do this we use new, multi-modal and integrative approaches that will:1.Evaluate the immediate effects of head trauma in youth 2.Monitor the resolution of post-concussion symptoms (PCS) and cognitive performance during recovery 3.Utilize new methods to verify brain injury and recoveryTo achieve our goals, we have implemented the Head Impact Telemetry (HIT) System. (Simbex; Lebanon, NH, USA). This system equips commercially available Easton S9 hockey helmets (Easton-Bell Sports; Van Nuys, CA, USA) with single-axis accelerometers designed to measure real-time head accelerations during contact sport participation ^{3 - 5}. By using telemetric technology, the magnitude of acceleration and location of all head impacts during sport participation can be objectively detected and recorded. We also use functional magnetic resonance imaging (fMRI) to localize and assess changes in neural activity specifically in the medial temporal and frontal lobes during the performance of cognitive tasks, since those are the cerebral regions most sensitive to concussive head injury ⁶. Finally, we are acquiring structural imaging data sensitive to damage in brain white matter.Download video file.^{(44M, mov)}     

Novel molecular and computational methods improve the accuracy of insertion site analysis in Sleeping Beauty-induced tumors

The recent development of the Sleeping Beauty (SB) system has led to the development of novel mouse models of cancer. Unlike spontaneous models, SB causes cancer through the action of mutagenic transposons that are mobilized in the genomes of somatic cells to induce mutations in cancer genes. While previous methods have successfully identified many transposon-tagged mutations in SB-induced tumors, limitations in DNA sequencing technology have prevented a comprehensive analysis of large tumor cohorts. Here we describe a novel method for producing genetic profiles of SB-induced tumors using Illumina sequencing. This method has dramatically increased the number of transposon-induced mutations identified in each tumor sample to reveal a level of genetic complexity much greater than previously appreciated. In addition, Illumina sequencing has allowed us to more precisely determine the depth of sequencing required to obtain a reproducible signature of transposon-induced mutations within tumor samples. The use of Illumina sequencing to characterize SB-induced tumors should significantly reduce sampling error that undoubtedly occurs using previous sequencing methods. As a consequence, the improved accuracy and precision provided by this method will allow candidate cancer genes to be identified with greater confidence. Overall, this method will facilitate ongoing efforts to decipher the genetic complexity of the human cancer genome by providing more accurate comparative information from Sleeping Beauty models of cancer.     

Relationship between exercise capacity and brain size in mammals

Background

A great deal of experimental research supports strong associations between exercise, cognition, neurogenesis and neuroprotection in mammals. Much of this work has focused on neurogenesis in individual subjects in a limited number of species. However, no study to date has examined the relationship between exercise and neurobiology across a wide range of mammalian taxa. It is possible that exercise and neurobiology are related across evolutionary time. To test this hypothesis, this study examines the association between exercise and brain size across a wide range of mammals.

Methodology/Principal Findings

Controlling for associations with body size, we examined the correlation between brain size and a proxy for exercise frequency and capacity, maximum metabolic rate (MMR; ml O₂ min⁻¹). We collected brain sizes and MMRs from the literature and calculated residuals from the least-squares regression line describing the relationship between body mass and each variable of interest. We then analyzed the correlation between residual brain size and residual MMR both before and after controlling for phylogeny using phylogenetic independent contrasts. We found a significant positive correlation between maximum metabolic rate and brain size across a wide range of taxa.

Conclusions

These results suggest a novel hypothesis that links brain size to the evolution of locomotor behaviors in a wide variety of mammalian species. In the end, we suggest that some portion of brain size in nonhuman mammals may have evolved in conjunction with increases in exercise capacity rather than solely in response to selection related to cognitive abilities.