Fork reversal and ssDNA accumulation at stalled replication forks owing to checkpoint defects

Checkpoint-mediated control of replicating chromosomes is essential for preventing cancer. In yeast, Rad53 kinase protects stalled replication forks from pathological rearrangements. To characterize the mechanisms controlling fork integrity, we analyzed replication intermediates formed in response to replication blocks using electron microscopy. At the forks, wild-type cells accumulate short single-stranded regions, which likely causes checkpoint activation, whereas rad53 mutants exhibit extensive single-stranded gaps and hemi-replicated intermediates, consistent with a lagging-strand synthesis defect. Further, rad53 cells accumulate Holliday junctions through fork reversal. We speculate that, in checkpoint mutants, abnormal replication intermediates begin to form because of uncoordinated replication and are further processed by unscheduled recombination pathways, causing genome instability.     

Electronic liquid crystal state in the high-temperature superconductor YBa2Cu3O6.45

Electronic phases with symmetry properties matching those of conventional liquid crystals have recently been discovered in transport experiments on semiconductor heterostructures and metal oxides at millikelvin temperatures. We report the spontaneous onset of a one-dimensional, incommensurate modulation of the spin system in the high-transition-temperature superconductor YBa2Cu3O6.45 upon cooling below approximately 150 kelvin, whereas static magnetic order is absent above 2 kelvin. The evolution of this modulation with temperature and doping parallels that of the in-plane anisotropy of the resistivity, indicating an electronic nematic phase that is stable over a wide temperature range. The results suggest that soft spin fluctuations are a microscopic route toward electronic liquid crystals and that nematic order can coexist with high-temperature superconductivity in underdoped cuprates.     

Saturation of the southern ocean CO2 sink due to recent climate change

Based on observed atmospheric carbon dioxide (CO2) concentration and an inverse method, we estimate that the Southern Ocean sink of CO2 has weakened between 1981 and 2004 by 0.08 petagrams of carbon per year per decade relative to the trend expected from the large increase in atmospheric CO2. We attribute this weakening to the observed increase in Southern Ocean winds resulting from human activities, which is projected to continue in the future. Consequences include a reduction of the efficiency of the Southern Ocean sink of CO2 in the short term (about 25 years) and possibly a higher level of stabilization of atmospheric CO2 on a multicentury time scale.     

The role of endosymbiotic Wolbachia bacteria in the pathogenesis of river blindness

Parasitic filarial nematodes infect more than 200 million individuals worldwide, causing debilitating inflammatory diseases such as river blindness and lymphatic filariasis. Using a murine model for river blindness in which soluble extracts of filarial nematodes were injected into the corneal stroma, we demonstrated that the predominant inflammatory response in the cornea was due to species of endosymbiotic Wolbachia bacteria. In addition, the inflammatory response induced by these bacteria was dependent on expression of functional Toll-like receptor 4 (TLR4) on host cells.     

Genome-wide insertional mutagenesis of Arabidopsis thaliana

Over 225,000 independent Agrobacterium transferred DNA (T-DNA) insertion events in the genome of the reference plant Arabidopsis thaliana have been created that represent near saturation of the gene space. The precise locations were determined for more than 88,000 T-DNA insertions, which resulted in the identification of mutations in more than 21,700 of the approximately 29,454 predicted Arabidopsis genes. Genome-wide analysis of the distribution of integration events revealed the existence of a large integration site bias at both the chromosome and gene levels. Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene.     

A molecular organic carbon isotope record of miocene climate changes

The difference in carbon-13 ((13)C) contents of hopane and sterane biomarkers in the Monterey formation (Naples Beach, California) parallels the Miocene inorganic record of the change in (18)O (delta(18)O), reflecting the Miocene evolution from a well-mixed to a highly stratified photic zone (upper 100 meters) in the Pacific. Steranes (delta(13)C = 25.4 +/- 0.7 per mil versus the Pee Dee belemnite standard) from shallow photic-zone organisms do not change isotopically throughout the Miocene. In contrast, sulfur-bound C(35) hopanes (likely derived from bacterial plankton living at the base of the photic zone) have systematically decreasing (13)C concentrations in Middle and Late Miocene samples (delta(13)C = -29.5 to -31.5 per mil), consistent with the Middle Miocene formation of a carbon dioxide-rich cold water mass at the base of the photic zone.     

On the origin of leprosy

Leprosy, a chronic human disease with potentially debilitating neurological consequences, results from infection with Mycobacterium leprae. This unculturable pathogen has undergone extensive reductive evolution, with half of its genome now occupied by pseudogenes. Using comparative genomics, we demonstrated that all extant cases of leprosy are attributable to a single clone whose dissemination worldwide can be retraced from analysis of very rare single-nucleotide polymorphisms. The disease seems to have originated in Eastern Africa or the Near East and spread with successive human migrations. Europeans or North Africans introduced leprosy into West Africa and the Americas within the past 500 years.     

Genome of Geobacter sulfurreducens: metal reduction in subsurface environments

The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments. As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity.     

Glutamate receptor-like genes form Ca2+ channels in pollen tubes and are regulated by pistil D-serine

Elevations in cytosolic free calcium concentration ([Ca(2+)](cyt)) constitute a fundamental signal transduction mechanism in eukaryotic cells, but the molecular identity of Ca(2+) channels initiating this signal in plants is still under debate. Here, we show by pharmacology and loss-of-function mutants that in tobacco and Arabidopsis, glutamate receptor-like channels (GLRs) facilitate Ca(2+) influx across the plasma membrane, modulate apical [Ca(2+)](cyt) gradient, and consequently affect pollen tube growth and morphogenesis. Additionally, wild-type pollen tubes grown in pistils of knock-out mutants for serine-racemase (SR1) displayed growth defects consistent with a decrease in GLR activity. Our findings reveal a novel plant signaling mechanism between male gametophyte and pistil tissue similar to amino acid-mediated communication commonly observed in animal nervous systems.     

A molecular switch and proton wire synchronize the active sites in thiamine enzymes

Thiamine diphosphate (ThDP) is used as a cofactor in many key metabolic enzymes. We present evidence that the ThDPs in the two active sites of the E1 (EC 1.2.4.1) component of the pyruvate dehydrogenase complex communicate over a distance of 20 angstroms by reversibly shuttling a proton through an acidic tunnel in the protein. This "proton wire" permits the co-factors to serve reciprocally as general acid/base in catalysis and to switch the conformation of crucial active-site peptide loops. This synchronizes the progression of chemical events and can account for the oligomeric organization, conformational asymmetry, and "ping-pong" kinetic properties of E1 and other thiamine-dependent enzymes.