Challenges of modeling ocean basin ecosystems

With increasing pressure for a more ecological approach to marine fisheries and environmental management, there is a growing need to understand and predict changes in marine ecosystems. Biogeochemical and physical oceanographic models are well developed, but extending these further up the food web to include zooplankton and fish is a major challenge. The difficulty arises because organisms at higher trophic levels are longer lived, with important variability in abundance and distribution at basin and decadal scales. Those organisms at higher trophic levels also have complex life histories compared to microbes, further complicating their coupling to lower trophic levels and the physical system. We discuss a strategy that builds on recent advances in modeling and observations and suggest a way forward that includes approaches to coupling across trophic levels and the inclusion of uncertainty.     

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster

Comparison of the genomes and proteomes of the two diptera Anopheles gambiae and Drosophila melanogaster, which diverged about 250 million years ago, reveals considerable similarities. However, numerous differences are also observed; some of these must reflect the selection and subsequent adaptation associated with different ecologies and life strategies. Almost half of the genes in both genomes are interpreted as orthologs and show an average sequence identity of about 56%, which is slightly lower than that observed between the orthologs of the pufferfish and human (diverged about 450 million years ago). This indicates that these two insects diverged considerably faster than vertebrates. Aligned sequences reveal that orthologous genes have retained only half of their intron/exon structure, indicating that intron gains or losses have occurred at a rate of about one per gene per 125 million years. Chromosomal arms exhibit significant remnants of homology between the two species, although only 34% of the genes colocalize in small "microsyntenic" clusters, and major interarm transfers as well as intra-arm shuffling of gene order are detected.     

A Burkholderia pseudomallei toxin inhibits helicase activity of translation factor eIF4A

The structure of BPSL1549, a protein of unknown function from Burkholderia pseudomallei, reveals a similarity to Escherichia coli cytotoxic necrotizing factor 1. We found that BPSL1549 acted as a potent cytotoxin against eukaryotic cells and was lethal when administered to mice. Expression levels of bpsl1549 correlate with conditions expected to promote or suppress pathogenicity. BPSL1549 promotes deamidation of glutamine-339 of the translation initiation factor eIF4A, abolishing its helicase activity and inhibiting translation. We propose to name BPSL1549 Burkholderia lethal factor 1.     

Radioactive elements on Mercury's surface from MESSENGER: implications for the planet's formation and evolution

The MESSENGER Gamma-Ray Spectrometer measured the average surface abundances of the radioactive elements potassium (K, 1150 ± 220 parts per million), thorium (Th, 220 ± 60 parts per billion), and uranium (U, 90 ± 20 parts per billion) in Mercury's northern hemisphere. The abundance of the moderately volatile element K, relative to Th and U, is inconsistent with physical models for the formation of Mercury requiring extreme heating of the planet or its precursor materials, and supports formation from volatile-containing material comparable to chondritic meteorites. Abundances of K, Th, and U indicate that internal heat production has declined substantially since Mercury's formation, consistent with widespread volcanism shortly after the end of late heavy bombardment 3.8 billion years ago and limited, isolated volcanic activity since.     

Association of TALS developmental disorder with defect in minor splicing component U4atac snRNA

The spliceosome, a ribonucleoprotein complex that includes proteins and small nuclear RNAs (snRNAs), catalyzes RNA splicing through intron excision and exon ligation to produce mature messenger RNAs, which, in turn serve as templates for protein translation. We identified four point mutations in the U4atac snRNA component of the minor spliceosome in patients with brain and bone malformations and unexplained postnatal death [microcephalic osteodysplastic primordial dwarfism type 1 (MOPD 1) or Taybi-Linder syndrome (TALS); Mendelian Inheritance in Man ID no. 210710]. Expression of a subgroup of genes, possibly linked to the disease phenotype, and minor intron splicing were affected in cell lines derived from TALS patients. Our findings demonstrate a crucial role of the minor spliceosome component U4atac snRNA in early human development and postnatal survival.     

Comment on "Absence of cooling in New Zealand and the adjacent ocean during the Younger Dryas chronozone"

Barrows et al. (Reports, 5 October 2007, p. 86) presented cosmogenic exposure dates and data from an ocean sediment core that challenge evidence for glacier advance in New Zealand during the Younger Dryas event. We use modeling of geomorphic processes to argue that their cosmogenic exposure dates are inconclusive.     

Long-term trends in the abundance of Mediterranean wetland vertebrates: From global recovery to localized declines

Biodiversity loss is unevenly distributed in space and time. Species have reached critically low population sizes in some areas, and remain abundant in others. Similarly, some species may benefit from successful conservation plans, while others still experience severe population depletions driven by negative impacts of human activities. Although several indicators have been proposed to measure the fate of biodiversity, they are generally only implemented globally so their relevance for regional assessment is still unclear. Here, we calculated the first regional trend in the Living Planet Index for the Mediterranean wetlands (Med LPI), an indicator that summarizes the fate of global biological diversity based on the temporal trends in abundance of vertebrate populations. The Med LPI was based on 1641 vertebrate populations of 311 species recorded in Mediterranean wetlands from 1970–2008, in 27 different countries. We investigated whether trends in the Med LPI differed between eastern and western Mediterranean countries, which have different socio-economic contexts. Finally, we assessed whether and how the trend in the Med LPI was robust to changes in the number and identity of species considered. We found that, at the Mediterranean scale, the Med LPI increased steeply, which could be taken at first sight, as a general recovery of wetland biodiversity in this biogeographical region. However, we found highly contrasting spatial trends within the Mediterranean region: the average trend was positive for western and negative for eastern countries. Moreover, we showed that depending on the method used to estimate the trend in Med LPI, it can be sensitive to the number and identity of the species considered. We suggest that understanding the regional discrepancies of the trend in biodiversity indicators as well as their robustness to the species represented in the index will enhance progress assessment towards global and regional conservation strategies.     

Elephant-induced structural changes in the vegetation and habitat selection by large herbivores in an African savanna

African elephants can affect the quality of the habitat of other species by breaking or uprooting trees and shrubs in savannas. Their effect on vegetation has been widely studied but less is known about the effects of such vegetation changes on other animals. We studied how changes in the vegetation caused by elephants influence the selection of microhabitats by five African herbivore species (giraffe, kudu, steenbok, impala, and zebra) in Hwange National Park, Zimbabwe. There was no clear significant effect of overall elephant-induced vegetation changes on microhabitat selection except for the small species (steenbok and impala) that used vegetation modified by elephants preferentially. This is consistent with a medium-term browsing facilitation hypothesis. More subtle possible effects were detected for larger browsers (giraffe and kudu). They selected areas with broken and uprooted plants and avoided coppiced areas. All of the browsers selected sites characterized by plants uprooted and broken by elephants, which were associated with a higher visibility, and ultimately a better probability of detecting an approaching predator, suggesting that perceived predation risk plays an important role in microhabitat selection. These results illustrate how elephants can initiate indirect effects that influence microhabitat selection by other herbivores. Understanding the indirect effects of elephants through changes in food availability and predation risk thus needs further investigation. The results of this study do not provide support for the hypothesis that elephant-induced changes in the structure of habitats have caused the declines in the populations of the other herbivores in the study area.