The extent of linkage disequilibrium in Arabidopsis thaliana.

Linkage disequilibrium (LD), the nonrandom occurrence of alleles in haplotypes, has long been of interest to population geneticists. Recently, the rapidly increasing availability of genomic polymorphism data has fueled interest in LD as a tool for fine-scale mapping, in particular for human disease loci. The chromosomal extent of LD is crucial in this context, because it determines how dense a map must be for associations to be detected and, conversely, limits how finely loci may be mapped. Arabidopsis thaliana is expected to harbor unusually extensive LD because of its high degree of selfing. Several polymorphism studies have found very strong LD within individual loci, but also evidence of some recombination. Here we investigate the pattern of LD on a genomic scale and show that in global samples, LD decays within approximately 1 cM, or 250 kb. We also show that LD in local populations may be much stronger than that of global populations, presumably as a result of founder events. The combination of a relatively high level of polymorphism and extensive haplotype structure bodes well for developing a genome-wide LD map in A. thaliana.     

Palaeolake and palaeoenvironment between 42 and 18 kaBP in tengger desert, NW China

Comprehensive field investigations and laboratory analyses show that palaeolakes, including fresh- mesohaline water Megalake Tengger and other semi-con- nected, isolated water bodies, during late Pleistocene covered an area of more than 20000 km², which is more than half of the Tengger Desert in NW China. Stratigraphic correlation and chronological evidence indicate that before ca. 42000 aBP the area was more arid. The palaeolakes started to develop around 40000 uncal. ¹⁴C aBP but until 37000 ¹⁴C aBP their scope was limited. High water levels established from 35000 ¹⁴C aBP lasted until 22000 ¹⁴CaBP. Lake levels regressed between 22000 and 20000 ¹⁴C aBP but transgressed from 20000 to 18600 ¹⁴C aBP. Subsequently, water level declined further and the Megalake Tengger finally desiccated at around 18000 ¹⁴C aBP. Megalake Tengger possessed a fresh-mesohaline water property, implying that the regional precipitation increased significantly. During the period of Megalake Tengger, the climate was warmer-humid than present. The annual rainfall was 250 to 350 mm more than that of today and the temperature was 1.5 to 3.0℃ higher.     

Mass march of termites into the deadly trap.

Carnivorous pitcher plants of the genus Nepenthes are not usually very selective about their prey, catching anything that is careless enough to walk on their slippery peristome, but Nepenthes albomarginata is an exception. We show here that this plant uses a fringe of edible white hairs to lure and then trap its prey, which consists exclusively of termites in enormous numbers. This singular feature accounts for the specialization of N. albomarginata for one prey taxon, unique so far among carnivorous plants.     

Superoxide activates mitochondrial uncoupling proteins.

Uncoupling protein 1 (UCP1) diverts energy from ATP synthesis to thermogenesis in the mitochondria of brown adipose tissue by catalysing a regulated leak of protons across the inner membrane. The functions of its homologues, UCP2 and UCP3, in other tissues are debated. UCP2 and UCP3 are present at much lower abundance than UCP1, and the uncoupling with which they are associated is not significantly thermogenic. Mild uncoupling would, however, decrease the mitochondrial production of reactive oxygen species, which are important mediators of oxidative damage. Here we show that superoxide increases mitochondrial proton conductance through effects on UCP1, UCP2 and UCP3. Superoxide-induced uncoupling requires fatty acids and is inhibited by purine nucleotides. It correlates with the tissue expression of UCPs, appears in mitochondria from yeast expressing UCP1, and is absent in skeletal muscle mitochondria from UCP3 knockout mice. Our findings indicate that the interaction of superoxide with UCPs may be a mechanism for decreasing the concentrations of reactive oxygen species inside mitochondria.     

Rutile U-Pb age for the ultra-high pressure eclogite from the dabie Mountains,central China:Evideence for rapid cooling

The U-Pb isotope compositions of rutile, omphacite and garnet in the eclogite from the Jinheqiao area in the Southern Dabie ultrahigh-pressure metamorphic zone were analyzed. The consistent high precision U-Pb age (218 ±(1.2) Ma of rutile in eclogite from the Dabie Mountains was obtained by two ways of isochron and common Pb correction based on the composition of omphacite. This proves that the omphacite in eclogite has a U/Pb ratio (μ = 2.8) low enough to be used for common Pb correction in the analyses of rutile. Under the rapid cooling condition (40℃/Ma) the closure temperature for U-Pb diffusion in rutile is about 470℃. Thus, this U-Pb age of rutile proves that 218 Ma should be the cooling age of eclogite at 470℃ instead of the peak metamorphic age.     

Deconstructing maize population structure.

Association studies have rarely been used in plant genetics, in part because of the risk of false positives caused by population structure. A study of flowering time in maize makes the first use of recent 'structured association' methods-statistical approaches that use independent loci to control for the effects of structure and admixture.     

Mutations in a human homologue of Drosophila crumbs cause retinitis pigmentosa (RP12).

Retinitis pigmentosa (RP) comprises a clinically and genetically heterogeneous group of diseases that afflicts approximately 1.5 million people worldwide. Affected individuals suffer from a progressive degeneration of the photoreceptors, eventually resulting in severe visual impairment. To isolate candidate genes for chorioretinal diseases, we cloned cDNAs specifically or preferentially expressed in the human retina and the retinal pigment epithelium (RPE) through a novel suppression subtractive hybridization (SSH) method. One of these cDNAs (RET3C11) mapped to chromosome 1q31-q32.1, a region harbouring a gene involved in a severe form of autosomal recessive RP characterized by a typical preservation of the para-arteriolar RPE (RP12; ref. 3). The full-length cDNA encodes an extracellular protein with 19 EGF-like domains, 3 laminin A G-like domains and a C-type lectin domain. This protein is homologous to the Drosophila melanogaster protein crumbs (CRB), and denoted CRB1 (crumbs homologue 1). In ten unrelated RP patients with preserved para-arteriolar RPE, we identified a homozygous AluY insertion disrupting the ORF, five homozygous missense mutations and four compound heterozygous mutations in CRB1. The similarity to CRB suggests a role for CRB1 in cell-cell interaction and possibly in the maintenance of cell polarity in the retina. The distinct RPE abnormalities observed in RP12 patients suggest that CRB1 mutations trigger a novel mechanism of photoreceptor degeneration.     

Susceptibility to testicular germ-cell tumours in a 129.MOLF-Chr 19 chromosome substitution strain.

The identification of genes that control susceptibility to testicular germ-cell tumours (TGCTs), the most common cancer affecting young men, has been difficult. In laboratory mice, TGCTs arise from primordial germ cells in only the 129 inbred strains, and susceptibility is under multigenic control. The spontaneously arising mutation Ter (ref. 5) on mouse chromosome 18 (Refs 6,7) increases TGCT frequency on a 129/Sv background. We originally used Ter in genetic crosses to identify loci that control tumorigenesis. A genome scan of tumour-bearing progeny from backcrosses between the 129/Sv-Ter/+ and MOLF/Ei strains provided modest evidence that MOLF-derived alleles on chromosome 19 enhance development of bilateral TGCTs (ref. 9). To obtain independent evidence for linkage to the MOLF chromosome, we made an autosomal chromosome substitution strain (CSS; or 'consomic strain') in which chromosome 19 of 129/Sv+/+ was replaced by its MOLF-derived homologue. The unusually high frequency of TGCTs in this CSS (even in the absence of the Ter mutation) provides evidence confirming the genome survey results, identifies linkage for a naturally occurring strain variant allele that confers susceptibility to TGCTs and illustrates the power of CSSs in complex trait analysis.