Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

Background  

Structural genomics projects such as the Protein Structure Initiative (PSI) yield many new structures, but often these have no known molecular functions. One approach to recover this information is to use 3D templates – structure-function motifs that consist of a few functionally critical amino acids and may suggest functional similarity when geometrically matched to other structures. Since experimentally determined functional sites are not common enough to define 3D templates on a large scale, this work tests a computational strategy to select relevant residues for 3D templates.     

Post-Flood Recovery of a Macroinvertebrate Community in a Regulated River: Resilience of an Anthropogenically Altered Ecosystem

Preservation of biodiversity depends on restoring the full range of historic environmental variation to which organisms have evolved, including natural disturbances. Lotic ecosystems have been fragmented by dams causing a reduction in natural levels of environmental variation (flow and temperature) and consequently a reduction of biodiversity in downstream communities. We conducted a long‐term study of the macroinvertebrate communities before and after natural flood disturbances in an unregulated reference site (natural flows and temperatures), a regulated site (regulated flows and temperatures), and a partially regulated reference site (regulated flows and natural temperatures) on the upper Colorado River downstream from a deep‐release storage reservoir. We aimed to test the hypothesis that floods and temperature restoration would cause an increase in macroinvertebrate diversity at the regulated site. Over the short term, macroinvertebrate richness decreased at the regulated site when compared to pre‐flood levels, whereas total macroinvertebrate density remained unchanged. Over the long term (1 and 10 years after the floods), macroinvertebrate diversity and community structure at the regulated site returned to pre‐flood levels without increasing to reference conditions. Occasional floods did not restore biodiversity in this system. As long as the physical state variables remain altered beyond a threshold, the community will return to its altered regulated condition. However, temperature restoration at the partially regulated site resulted in an increase in macroinvertebrate diversity. Our results indicate that restoration of the natural temperature regime will have a stronger effect on restoring biodiversity than occasional channel‐forming floods.     

Monomeric M2e antigen in VesiVax® liposomes stimulates protection against type a strains of influenza comparable to liposomes with multimeric forms of M2e

Abstract

Given the interest in the ectodomain of the matrix 2 (M2e) channel protein as a target for development of a universal influenza vaccine, we examined the role of the antigen configuration of M2e in generating a protective immune response. A series of M2e mutations and a truncated M2e segment were prepared as a means of controlling the formation of monomer, dimer, and higher order multimeric forms of M2e. Each of these M2e peptides was incorporated into a liposome-based vaccine technology platform previously shown to stimulate a protective response to influenza A infection using M2e as a mixture of monomers, dimers and multimers (L-M2e1-HD/MPL). Our results using these modified forms of M2e produced 90–100% survival following lethal challenge with H1N1 (A/PR/8/34) in both inbred BALB/c and outbred Swiss Webster mice vaccinated with a truncated monomeric form of the M2 protein, M2e_1–15 in liposomes. These observations show that a tetrameric configuration is not required to elicit significant protection when the M2e antigen is formulated in immunogenic liposomes and further, that the first 15 amino acids of M2e likely play a primary role in providing the protective immune response.     

Variation in nestling body condition and wing development predict cause‐specific mortality in fledgling dickcissels

Phenotypic traits developed in one life‐history stage can carryover and affect survival in subsequent stages. For songbirds, carryover effects from the pre‐ to post‐fledging period may be crucial for survival but are poorly understood. We assessed whether juvenile body condition and wing development at fledging influenced survival during the post‐fledging period in the dickcissel Spiza americana. We found pre‐ to post‐fledging carryover effects on fledgling survival for both traits during the ‘early part’ – first four days – of the post‐fledging period. Survival benefits of each trait depended on cause‐specific sources of mortality; individuals in better body condition were less likely to die from exposure to adverse environmental conditions, whereas those with more advanced wing development were less likely to be preyed upon. Fledglings with more advanced wing development were comparatively more active and mobile earlier in the post‐fledging period, suggesting they were better able to avoid predators. Our results provide some of the first evidence linking development of juvenile phenotypic traits to survival against specific sources of post‐fledging mortality in songbirds. Further investigation into pre‐ to post‐fledging carryover effects may yield important insights into avian life‐history evolution.     

Crown group Oxyphotobacteria postdate the rise of oxygen

The rise of oxygen ca. 2.3 billion years ago (Ga) is the most distinct environmental transition in Earth history. This event was enabled by the evolution of oxygenic photosynthesis in the ancestors of Cyanobacteria. However, long‐standing questions concern the evolutionary timing of this metabolism, with conflicting answers spanning more than one billion years. Recently, knowledge of the Cyanobacteria phylum has expanded with the discovery of non‐photosynthetic members, including a closely related sister group termed Melainabacteria, with the known oxygenic phototrophs restricted to a clade recently designated Oxyphotobacteria. By integrating genomic data from the Melainabacteria, cross‐calibrated Bayesian relaxed molecular clock analyses show that crown group Oxyphotobacteria evolved ca. 2.0 billion years ago (Ga), well after the rise of atmospheric dioxygen. We further estimate the divergence between Oxyphotobacteria and Melainabacteria ca. 2.5–2.6 Ga, which—if oxygenic photosynthesis is an evolutionary synapomorphy of the Oxyphotobacteria—marks an upper limit for the origin of oxygenic photosynthesis. Together, these results are consistent with the hypothesis that oxygenic photosynthesis evolved relatively close in time to the rise of oxygen.     

Assessment of cues potentially mediating host selection of Leptoglossus occidentalis on Pinus contorta

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An invasive tree facilitates the persistence of native rodents on an over‐grazed floodplain in tropical Australia

In an ecosystem under simultaneous threat from multiple alien species, one invader may buffer the impact of another. Our surveys on a remote floodplain in the Kimberley region of north western Australia show that invasive chinee apple trees (Ziziphus mauritiana) provide critical refuge habitat for native rodents (pale field rats, Rattus tunneyi). Feral horses (Equus caballus) have trampled most of the remaining floodplain, but are excluded from the area around each chinee apple tree by thorny foliage. Although chinee apple trees constituted <10% of trees along our transects, they represented >50% of trees that harboured rat burrows. The mean number of burrows under each chinee apple tree was twice as high as under most other tree species, and we trapped more than seven times as many rats under chinee apple trees as under other types of trees. The extensive burrow systems under chinee apple trees contained female as well as male rats, whereas we only captured males around the smaller burrow systems under other tree species. Our data suggest that this invasive tree plays a critical role in the persistence of pale field rat populations in this degraded ecosystem, and that managers should maintain these trees (despite their alien origins) at least until feral horses have been removed.