Protein Interaction Networks

The study of protein interactions is playing an ever increasing role in our attempts to understand cells and diseases on a system-wide level. This article reviews several experimental approaches that are currently being used to measure protein–protein, protein–DNA and gene–gene interactions. These techniques have now been scaled up to produce extensive genome-wide data sets that are providing us with a first glimpse of global interaction networks. Complementing these experimental approaches, several computational methodologies to predict protein interactions are also reviewed. Existing databases that serve as repositories for protein interaction information and how such databases are used to analyze high-throughput data from a pathway perspective is also addressed. Finally, current efforts to combine multiple data types to obtain more accurate and comprehensive models of protein interactions are discussed. It is clear that the evolution of these experimental and computational approaches is rapidly changing our view of biology, and promises to provide us with an unprecedented ability to model cells and organisms at a system-wide level.     

Biodiversity curves for the Ordovician of Baltoscandia

Biodiversity curves for the Ordovician of Baltoscandia show a substantial increase in taxonomical diversity through the period, as seen also in global data sets. A database of 10,340 records of first and last appearances of species at different localities in the region has been analysed using simple species counts, and partly validated with resampling methods. While the biodiversity curve for all fossil groups combined is probably reasonably accurate except for an unknown scaling constant, taxonomical or geographical subsets may not be sufficiently well sampled to allow precise measurement of their species counts through time. The analysis shows a major diversification event commencing in the middle Arenig (Ibex-Whiterock boundary), and more limited diversification events in the Llanvirn, Caradoc and Ashgill. The Scandinavian (Norwegian and Swedish) biodiversity curves are broadly correlated with major changes in sea level, with low biodiversity at highstands and high biodiversity at lowstands, although this pattern is not clear for all fossil groups. In the Arenig, graptolites and trilobites appear to have higher diversities at high sea levels, while the brachiopods and ostracodes show higher diversities at low sea level. As a consequence, the Arenig diversification is delayed for the latter two groups until the upper end of the interval.     

Taphonomic and paleoecological change in the large mammal sequence from Boomplaas Cave,western Cape,South Africa

Excavations conducted by H.J. Deacon in the 1970s at Boomplaas Cave (BPA) uncovered a stratified sequence of Middle Stone Age (MSA) and Later Stone Age (LSA) deposits spanning the last >65,000 years. This study provides the first comprehensive and integrated taphonomic and paleoecological analysis of the BPA large mammals, with a focus on its implications for understanding human adaptations and environmental changes in southern Africa's Cape Floristic Region (CFR), an area that features prominently in understanding modern human origins. Taphonomic data indicate a complex history of human, carnivore, and raptor accumulation of the large mammal assemblage. The anthropogenic signal is largely absent from the bottom of the sequence (>65,000 years ago), intermediate in MSA and LSA assemblages from ∼50,000 to 20,000 years ago, and strong in LSA deposits post-dating the Last Glacial Maximum (LGM). When viewed in the broader CFR context, the inferred occupation history of BPA is consistent with the hypothesis that both MSA and LSA human populations were concentrated on the submerged coastline from ∼60,000 to ∼20,000 years ago. Intensive occupation following the LGM parallels an apparent increase in regional population densities, which may have been driven in part by rising sea levels. The BPA ungulate assemblage is characterized by the rise and decline of a taxonomically diverse grazing community, which peaks during the LGM. These changes are not correlated with taphonomic shifts, meaning that they are likely driven by environmental factors, namely the expansion and contraction of grassland habitats. Changes in ungulate diversity indicate that effective precipitation was highest during the LGM, corresponding with an intensified winter rainfall system. This is consistent with recent arguments that the LGM in this region may not have been extremely harsh and arid.     

Othonna cerarioides (Asteraceae: Othonnineae), a new species from Namaqualand,South Africa

Othonna cerarioides Magoswana and J.C. Manning is described as a new species from Namaqualand, Northern Cape Province of South Africa. It is an erect shrub with rod-like stems and branches, bearing numerous spur-shoots with obovate-oblanceolate leaves clustered at the tips, and up to nine disciform capitula per spur-shoot. Othonna cerarioides is anomalous in the genus in that the style of some of the disc florets is bifid. Othonna is diagnosed within subtribe Othonnineae by female-sterile disc florets with simple (or very rarely minutely bifid) styles. The disc florets in the closely related genus Hertia are bisexual with well branched styles.     

Resources available to individuals and organisations involved with marine turtle research and conservation in the Mediterranean

Abstract

We review some key resources freely or cheaply available to those involved with marine turtle research and conservation in the Mediterranean. These include: Marine Turtle Newsletter, Listservs, bibliographic databases, Mediterranean specific technical manuals, IUCN Marine Turtle Specialist Group publications, internet sources and books.     

Frequent and parallel habitat transitions as driver of unbounded radiations in the Cape flora

The enormous species richness in the Cape Floristic Region (CFR) of Southern Africa is the result of numerous radiations, but the temporal progression and possible mechanisms of these radiations are still poorly understood. Here, we explore the macroevolutionary dynamics of the Restionaceae, which include 340 species that are found in all vegetation types in the Cape flora and are ecologically dominant in fynbos. Using an almost complete (i.e., 98%) species‐level time calibrated phylogeny and models of diversification dynamics, we show that species diversification is constant through the Cenozoic, with no evidence of an acceleration with the onset of the modern winter‐wet climate, or a recent density‐dependent slowdown. Contrary to expectation, species inhabiting the oldest (montane) and most extensive (drylands) habitats did not undergo higher diversification rates than species in the younger (lowlands) and more restricted (wetland) habitats. We show that the rate of habitat transitions is more closely related to the speciation rate than to time, and that more than a quarter of all speciation events are associated with habitat transitions. This suggests that the unbounded Restionaceae diversification resulted from numerous, parallel, habitat shifts, rather than persistence in a habitat stimulating speciation. We speculate that this could be one of the mechanisms resulting in the hyperdiverse Cape flora.