Environment: early ant plagues in the New World

The identity and origin of the West Indian plague ants of the early sixteenth and late eighteenth centuries have long been a mystery. By reviewing historic accounts with an analysis of the present-day Caribbean ant fauna, I have narrowed the list of suspects to two species and their insect symbionts.     

Rapid stepwise onset of Antarctic glaciation and deeper calcite compensation in the Pacific Ocean

The ocean depth at which the rate of calcium carbonate input from surface waters equals the rate of dissolution is termed the calcite compensation depth. At present, this depth is approximately 4,500 m, with some variation between and within ocean basins. The calcite compensation depth is linked to ocean acidity, which is in turn linked to atmospheric carbon dioxide concentrations and hence global climate. Geological records of changes in the calcite compensation depth show a prominent deepening of more than 1 km near the Eocene/Oligocene boundary (approximately 34 million years ago) when significant permanent ice sheets first appeared on Antarctica, but the relationship between these two events is poorly understood. Here we present ocean sediment records of calcium carbonate content as well as carbon and oxygen isotopic compositions from the tropical Pacific Ocean that cover the Eocene/Oligocene boundary. We find that the deepening of the calcite compensation depth was more rapid than previously documented and occurred in two jumps of about 40,000 years each, synchronous with the stepwise onset of Antarctic ice-sheet growth. The glaciation was initiated, after climatic preconditioning, by an interval when the Earth's orbit of the Sun favoured cool summers. The changes in oxygen-isotope composition across the Eocene/Oligocene boundary are too large to be explained by Antarctic ice-sheet growth alone and must therefore also indicate contemporaneous global cooling and/or Northern Hemisphere glaciation.     

Optimal eye movement strategies in visual search

To perform visual search, humans, like many mammals, encode a large field of view with retinas having variable spatial resolution, and then use high-speed eye movements to direct the highest-resolution region, the fovea, towards potential target locations. Good search performance is essential for survival, and hence mammals may have evolved efficient strategies for selecting fixation locations. Here we address two questions: what are the optimal eye movement strategies for a foveated visual system faced with the problem of finding a target in a cluttered environment, and do humans employ optimal eye movement strategies during a search? We derive the ideal bayesian observer for search tasks in which a target is embedded at an unknown location within a random background that has the spectral characteristics of natural scenes. Our ideal searcher uses precise knowledge about the statistics of the scenes in which the target is embedded, and about its own visual system, to make eye movements that gain the most information about target location. We find that humans achieve nearly optimal search performance, even though humans integrate information poorly across fixations. Analysis of the ideal searcher reveals that there is little benefit from perfect integration across fixations--much more important is efficient processing of information on each fixation. Apparently, evolution has exploited this fact to achieve efficient eye movement strategies with minimal neural resources devoted to memory.     

Immunology: Insulin auto-antigenicity in type 1 diabetes

Spontaneous type 1 diabetes occurs when the autoimmune destruction of pancreatic beta-islet cells prevents production of the hormone insulin. This causes an inability to regulate glucose metabolism, which results in dangerously raised blood glucose concentrations. It is generally accepted that thymus-derived lymphocytes (T cells) are critically involved in the onset and progression of type 1 diabetes, but the antigens that initiate and drive this destructive process remain poorly characterized--although several candidates have been considered. Nakayama et al. and Kent et al. claim that insulin itself is the primary autoantigen that initiates spontaneous type 1 diabetes in mice and humans, respectively, a result that could have implications for more effective prevention and therapy. However, I believe that this proposed immunological role of insulin may be undermined by the atypical responses of T cells to the human insulin fragment that are described by Kent et al..     

A physical map of the chicken genome

Strategies for assembling large, complex genomes have evolved to include a combination of whole-genome shotgun sequencing and hierarchal map-assisted sequencing. Whole-genome maps of all types can aid genome assemblies, generally starting with low-resolution cytogenetic maps and ending with the highest resolution of sequence. Fingerprint clone maps are based upon complete restriction enzyme digests of clones representative of the target genome, and ultimately comprise a near-contiguous path of clones across the genome. Such clone-based maps are used to validate sequence assembly order, supply long-range linking information for assembled sequences, anchor sequences to the genetic map and provide templates for closing gaps. Fingerprint maps are also a critical resource for subsequent functional genomic studies, because they provide a redundant and ordered sampling of the genome with clones. In an accompanying paper we describe the draft genome sequence of the chicken, Gallus gallus, the first species sequenced that is both a model organism and a global food source. Here we present a clone-based physical map of the chicken genome at 20-fold coverage, containing 260 contigs of overlapping clones. This map represents approximately 91% of the chicken genome and enables identification of chicken clones aligned to positions in other sequenced genomes.     

Spatial patterns in species distributions reveal biodiversity change

Interpretation of global biodiversity change is hampered by a lack of information on the historical status of most species in most parts of the world. Here we show that declines and increases can be deduced from current species distributions alone, using spatial patterns of occupancy combined with distribution size. Declining species show sparse, fragmented distributions for their distribution size, reflecting the extinction process; expanding species show denser, more aggregated distributions, reflecting colonization. Past distribution size changes for British butterflies were deduced successfully from current distributions, and former distributions had some power to predict future change. What is more, the relationship between distribution pattern and change in British butterflies independently predicted distribution change for butterfly species in Flanders, Belgium, and distribution change in British rare plant species is similarly related to spatial distribution pattern. This link between current distribution patterns and processes of distribution change could be used to assess relative levels of threat facing different species, even for regions and taxa lacking detailed historical and ecological information.     

Regulation of p53 activity through lysine methylation

p53 is a tumour suppressor that regulates the cellular response to genotoxic stresses. p53 is a short-lived protein and its activity is regulated mostly by stabilization via different post-translational modifications. Here we report a novel mechanism of p53 regulation through lysine methylation by Set9 methyltransferase. Set9 specifically methylates p53 at one residue within the carboxyl-terminus regulatory region. Methylated p53 is restricted to the nucleus and the modification positively affects its stability. Set9 regulates the expression of p53 target genes in a manner dependent on the p53-methylation site. The crystal structure of a ternary complex of Set9 with a p53 peptide and the cofactor product S-adenosyl-l-homocysteine (AdoHcy) provides the molecular basis for recognition of p53 by this lysine methyltransferase.     

Analyses on the climate change responses over China under SRES B2 scenario using PRECIS

The global climate has been altered by the anthro- pogenic forcing due to greenhouse gases (GHGs) emis- sions. It is pointed out in the Third Assessments Report (TAR)[1] of Intergovernmental Panel on Climate Change (IPCC) in 2001 that over the 20th centur…