Tonks-Girardeau gas of ultracold atoms in an optical lattice

Strongly correlated quantum systems are among the most intriguing and fundamental systems in physics. One such example is the Tonks-Girardeau gas, proposed about 40 years ago, but until now lacking experimental realization; in such a gas, the repulsive interactions between bosonic particles confined to one dimension dominate the physics of the system. In order to minimize their mutual repulsion, the bosons are prevented from occupying the same position in space. This mimics the Pauli exclusion principle for fermions, causing the bosonic particles to exhibit fermionic properties. However, such bosons do not exhibit completely ideal fermionic (or bosonic) quantum behaviour; for example, this is reflected in their characteristic momentum distribution. Here we report the preparation of a Tonks-Girardeau gas of ultracold rubidium atoms held in a two-dimensional optical lattice formed by two orthogonal standing waves. The addition of a third, shallower lattice potential along the long axis of the quantum gases allows us to enter the Tonks-Girardeau regime by increasing the atoms' effective mass and thereby enhancing the role of interactions. We make a theoretical prediction of the momentum distribution based on an approach in which trapped bosons acquire fermionic properties, finding that it agrees closely with the measured distribution.     

C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression

To verify the genome annotation and to create a resource to functionally characterize the proteome, we attempted to Gateway-clone all predicted protein-encoding open reading frames (ORFs), or the 'ORFeome,' of Caenorhabditis elegans. We successfully cloned approximately 12,000 ORFs (ORFeome 1.1), of which roughly 4,000 correspond to genes that are untouched by any cDNA or expressed-sequence tag (EST). More than 50% of predicted genes needed corrections in their intron-exon structures. Notably, approximately 11,000 C. elegans proteins can now be expressed under many conditions and characterized using various high-throughput strategies, including large-scale interactome mapping. We suggest that similar ORFeome projects will be valuable for other organisms, including humans.     

Patterns of predation in a diverse predator-prey system

There are many cases where animal populations are affected by predators and resources in terrestrial ecosystems, but the factors that determine when one or the other predominates remain poorly understood. Here we show, using 40 years of data from the highly diverse mammal community of the Serengeti ecosystem, East Africa, that the primary cause of mortality for adults of a particular species is determined by two factors--the species diversity of both the predators and prey and the body size of that prey species relative to other prey and predators. Small ungulates in Serengeti are exposed to more predators, owing to opportunistic predation, than are larger ungulates; they also suffer greater predation rates, and experience strong predation pressure. A threshold occurs at prey body sizes of approximately 150 kg, above which ungulate species have few natural predators and exhibit food limitation. Thus, biodiversity allows both predation (top-down) and resource limitation (bottom-up) to act simultaneously to affect herbivore populations. This result may apply generally in systems where there is a diversity of predators and prey.     

Cenozoic climate change as a possible cause for the rise of the Andes

Causal links between the rise of a large mountain range and climate have often been considered to work in one direction, with significant uplift provoking climate change. Here we propose a mechanism by which Cenozoic climate change could have caused the rise of the Andes. Based on considerations of the force balance in the South American lithosphere, we suggest that the height of, and tectonics in, the Andes are strongly controlled both by shear stresses along the plate interface in the subduction zone and by buoyancy stress contrasts between the trench and highlands, and shear stresses in the subduction zone depend on the amount of subducted sediments. We propose that the dynamics of subduction and mountain-building in this region are controlled by the processes of erosion and sediment deposition, and ultimately climate. In central South America, climate-controlled sediment starvation would then cause high shear stress, focusing the plate boundary stresses that support the high Andes.     

Comparative analysis of the genome sequences of Bordetella pertussis,Bordetella parapertussis and Bordetella bronchiseptica

Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica are closely related Gram-negative beta-proteobacteria that colonize the respiratory tracts of mammals. B. pertussis is a strict human pathogen of recent evolutionary origin and is the primary etiologic agent of whooping cough. B. parapertussis can also cause whooping cough, and B. bronchiseptica causes chronic respiratory infections in a wide range of animals. We sequenced the genomes of B. bronchiseptica RB50 (5,338,400 bp; 5,007 predicted genes), B. parapertussis 12822 (4,773,551 bp; 4,404 genes) and B. pertussis Tohama I (4,086,186 bp; 3,816 genes). Our analysis indicates that B. parapertussis and B. pertussis are independent derivatives of B. bronchiseptica-like ancestors. During the evolution of these two host-restricted species there was large-scale gene loss and inactivation; host adaptation seems to be a consequence of loss, not gain, of function, and differences in virulence may be related to loss of regulatory or control functions.     

Maternal inhibition of hepatitis B surface antigen gene expression in transgenic mice correlates with de novo methylation

Differential modifications of the genome during gametogenesis result in a functional difference between the paternal and maternal genomes at the moment of fertilization. A possible cause of this imprinting is the methylation of DNA. The insertion of foreign DNA into transgenic mice allows the tagging of regions that are differentially methylated during gametogenesis. We describe here a transgenic mouse strain in which the expression of the hepatitis B surface antigen gene is irreversibly repressed following its passage through the female germ line. This inhibition is accompanied by the methylation of all the HpaII and HhaI sites within the foreign gene, which we have shown to be integrated into a site on chromosome 13. The irreversibility reported here contrasts with what is found with other transgenic mice sequences which are reversibly methylated after passage through the male or female germ line, though in both cases methylation appears to be important in the imprinting process.