Genome sequence and analysis of the tuber crop potato

Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.     

Truncating mutations in the Fanconi anemia J gene BRIP1 are low-penetrance breast cancer susceptibility alleles

We identified constitutional truncating mutations of the BRCA1-interacting helicase BRIP1 in 9/1,212 individuals with breast cancer from BRCA1/BRCA2 mutation-negative families but in only 2/2,081 controls (P = 0.0030), and we estimate that BRIP1 mutations confer a relative risk of breast cancer of 2.0 (95% confidence interval = 1.2-3.2, P = 0.012). Biallelic BRIP1 mutations were recently shown to cause Fanconi anemia complementation group J. Thus, inactivating truncating mutations of BRIP1, similar to those in BRCA2, cause Fanconi anemia in biallelic carriers and confer susceptibility to breast cancer in monoallelic carriers.     

Low-penetrance susceptibility to breast cancer due to CHEK2(*)1100delC in noncarriers of BRCA1 or BRCA2 mutations

Mutations in BRCA1 and BRCA2 confer a high risk of breast and ovarian cancer, but account for only a small fraction of breast cancer susceptibility. To find additional genes conferring susceptibility to breast cancer, we analyzed CHEK2 (also known as CHK2), which encodes a cell-cycle checkpoint kinase that is implicated in DNA repair processes involving BRCA1 and p53 (refs 3,4,5). We show that CHEK2(*)1100delC, a truncating variant that abrogates the kinase activity, has a frequency of 1.1% in healthy individuals. However, this variant is present in 5.1% of individuals with breast cancer from 718 families that do not carry mutations in BRCA1 or BRCA2 (P = 0.00000003), including 13.5% of individuals from families with male breast cancer (P = 0.00015). We estimate that the CHEK2(*)1100delC variant results in an approximately twofold increase of breast cancer risk in women and a tenfold increase of risk in men. By contrast, the variant confers no increased cancer risk in carriers of BRCA1 or BRCA2 mutations. This suggests that the biological mechanisms underlying the elevated risk of breast cancer in CHEK2 mutation carriers are already subverted in carriers of BRCA1 or BRCA2 mutations, which is consistent with participation of the encoded proteins in the same pathway.     

The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria

Bacillus anthracis is an endospore-forming bacterium that causes inhalational anthrax. Key virulence genes are found on plasmids (extra-chromosomal, circular, double-stranded DNA molecules) pXO1 (ref. 2) and pXO2 (ref. 3). To identify additional genes that might contribute to virulence, we analysed the complete sequence of the chromosome of B. anthracis Ames (about 5.23 megabases). We found several chromosomally encoded proteins that may contribute to pathogenicity--including haemolysins, phospholipases and iron acquisition functions--and identified numerous surface proteins that might be important targets for vaccines and drugs. Almost all these putative chromosomal virulence and surface proteins have homologues in Bacillus cereus, highlighting the similarity of B. anthracis to near-neighbours that are not associated with anthrax. By performing a comparative genome hybridization of 19 B. cereus and Bacillus thuringiensis strains against a B. anthracis DNA microarray, we confirmed the general similarity of chromosomal genes among this group of close relatives. However, we found that the gene sequences of pXO1 and pXO2 were more variable between strains, suggesting plasmid mobility in the group. The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis.     

Heart rate variability during high-intensity exercise

The aim of this paper is to describe and analyse the behaviour of heart rate variability (HRV) during constant-load, high-intensity exercise using a time frequency analysis (Wavelet Transform). Eleven elite cyclists took part in the study (age: 18.6±3.0 years; VO_2max: 4.88±0.61 litres·min^?1). Initially, all subjects performed an incremental cycloergometer test to determine load power in a constant load-test (379.55±36.02 W; 89.0%). HRV declined dramatically from the start of testing (p <0.05). The behaviour of power spectral density within the LF band mirrored that of total energy, recording a significant decrease from the outset LF peaks fell rapidly thereafter, remaining stable until the end of the test. HF-VHF fell sharply in the first 20 to 30 seconds. The relative weighting (%) of HF-VHF was inverted with the onset of fatigue, [1.6% at the start, 7.1 (p <0.05) at the end of the first phase, and 43.1% (p <0.05) at the end of the test]. HF-VHF_peak displayed three phases: a moderate initial increase, followed by a slight fall, thereafter increasing to the end of the test. The LF/HF-VHF ratio increased at the start, later falling progressively until the end of the first phase and remaining around minimal values until the end of the test.     

Clark's Nutcrackers harvest sugar pine seeds from cones

This is the first report of Clark&rsquo;s Nutcrackers ( Nucifraga columbiana ) harvesting seeds from the cones of sugar pine ( Pinus lambertiana ), based on observations over several years in Crater Lake National Park, Oregon. The harvesting period in late September corresponded to peak cone-opening dates. Nutcrackers placed harvested seeds in their throat pouches, a behavior associated with seed caching.     

Nesting ecology of Yellow Warblers ( Dendroica petechia ) in montane chaparral habitat in the northern Sierra Nevada

The Yellow Warbler ( Dendroica petechia ) is considered a riparian specialist in much of western North America, but in California it also breeds in a second habitat type: montane chaparral of the Sierra Nevada and southern Cascades. We monitored Yellow Warbler nests in montane chaparral and assessed their poorly known nesting ecology in this habitat. We also conducted point counts in upland habitat throughout the region. We determined habitat associations for Yellow Warblers based on nest site and point-count vegetation data; nests were predominantly in bush chinquapin ( Chrysolepis sempervirens ) and greenleaf manzanita ( Arctostaphylos patula ), and point-count abundance was most strongly associated with high overall shrub cover. The importance of montane chaparral for a number of shrub-dependent Sierran birds is well documented, yet the chaparral is threatened by various practices including fire suppression, closed-canopy-focused forest management, and understory fuels-reduction treatments. Although Yellow Warblers are far more abundant in wet mountain meadow riparian habitat in the region, we recommend that management of montane chaparral habitat consider this species and the requirements of other shrub-nesting birds.