A short-term sink for atmospheric CO2 in subtropical mode water of the North Atlantic Ocean

Large-scale features of ocean circulation, such as deep water formation in the northern North Atlantic Ocean, are known to regulate the long-term physical uptake of CO2 from the atmosphere by moving CO2-laden surface waters into the deep ocean. But the importance of CO2 uptake into water masses that ventilate shallower ocean depths, such as subtropical mode waters of the subtropical gyres, are poorly quantified. Here we report that, between 1988 and 2001, dissolved CO2 concentrations in subtropical mode waters of the North Atlantic have increased at a rate twice that expected from these waters keeping in equilibrium with increasing atmospheric CO2. This accounts for an extra 0.4-2.8 Pg C (1 Pg = 10(15) g) over this period (that is, about 0.03-0.24 Pg C yr(-1)), equivalent to 3-10% of the current net annual ocean uptake of CO2 (ref. 3). We suggest that the lack of strong winter mixing events, to greater than 300 m in depth, in recent decades is responsible for this accumulation, which would otherwise disturb the mode water layer and liberate accumulated CO2 back to the atmosphere. However, future climate variability (which influences subtropical mode water formation) and changes in the North Atlantic Oscillation (leading to a return of deep winter mixing events) may reduce CO2 accumulation in subtropical mode waters. We therefore conclude that, although CO2 uptake by subtropical mode waters in the North Atlantic--and possibly elsewhere--does not always represent a long-term CO2 sink, the phenomenon is likely to contribute substantially to interannual variability in oceanic CO2 uptake.     

Spintronics: spin accumulation in mesoscopic systems

In spintronics, in which use is made of the spin degree of freedom of the electron, issues concerning electrical spin injection and detection of electron spin diffusion are fundamentally important. Jedema et al. describe a magneto-resistance study in which they claim to have observed spin accumulation in a mesoscopic copper wire, but their one-dimensional model ignores two-dimensional spin-diffusion effects, which casts doubt on their analysis. A two-dimensional vector formalism of spin transport is called for to model spin-injection experiments, and the identification of spurious background resistance effects is crucial.     

Somatic activation of the K-ras oncogene causes early onset lung cancer in mice

About 30% of human tumours carry ras gene mutations. Of the three genes in this family (composed of K-ras, N-ras and H-ras), K-ras is the most frequently mutated member in human tumours, including adenocarcinomas of the pancreas ( approximately 70-90% incidence), colon ( approximately 50%) and lung ( approximately 25-50%). To construct mouse tumour models involving K-ras, we used a new gene targeting procedure to create mouse strains carrying oncogenic alleles of K-ras that can be activated only on a spontaneous recombination event in the whole animal. Here we show that mice carrying these mutations were highly predisposed to a range of tumour types, predominantly early onset lung cancer. This model was further characterized by examining the effects of germline mutations in the tumour suppressor gene p53, which is known to be mutated along with K-ras in human tumours. This approach has several advantages over traditional transgenic strategies, including that it more closely recapitulates spontaneous oncogene activation as seen in human cancers.     

Haplotype tagging for the identification of common disease genes

Genome-wide linkage disequilibrium (LD) mapping of common disease genes could be more powerful than linkage analysis if the appropriate density of polymorphic markers were known and if the genotyping effort and cost of producing such an LD map could be reduced. Although different metrics that measure the extent of LD have been evaluated, even the most recent studies have not placed significant emphasis on the most informative and cost-effective method of LD mapping-that based on haplotypes. We have scanned 135 kb of DNA from nine genes, genotyped 122 single-nucleotide polymorphisms (SNPs; approximately 184,000 genotypes) and determined the common haplotypes in a minimum of 384 European individuals for each gene. Here we show how knowledge of the common haplotypes and the SNPs that tag them can be used to (i) explain the often complex patterns of LD between adjacent markers, (ii) reduce genotyping significantly (in this case from 122 to 34 SNPs), (iii) scan the common variation of a gene sensitively and comprehensively and (iv) provide key fine-mapping data within regions of strong LD. Our results also indicate that, at least for the genes studied here, the current version of dbSNP would have been of limited utility for LD mapping because many common haplotypes could not be defined. A directed re-sequencing effort of the approximately 10% of the genome in or near genes in the major ethnic groups would aid the systematic evaluation of the common variant model of common disease.     

A novel pantothenate kinase gene (PANK2) is defective in Hallervorden-Spatz syndrome

Hallervorden-Spatz syndrome (HSS) is an autosomal recessive neurodegenerative disorder associated with iron accumulation in the brain. Clinical features include extrapyramidal dysfunction, onset in childhood, and a relentlessly progressive course. Histologic study reveals iron deposits in the basal ganglia. In this respect, HSS may serve as a model for complex neurodegenerative diseases, such as Parkinson disease, Alzheimer disease, Huntington disease and human immunodeficiency virus (HIV) encephalopathy, in which pathologic accumulation of iron in the brain is also observed. Thus, understanding the biochemical defect in HSS may provide key insights into the regulation of iron metabolism and its perturbation in this and other neurodegenerative diseases. Here we show that HSS is caused by a defect in a novel pantothenate kinase gene and propose a mechanism for oxidative stress in the pathophysiology of the disease.     

Positive selection of a gene family during the emergence of humans and African apes

Gene duplication followed by adaptive evolution is one of the primary forces for the emergence of new gene function. Here we describe the recent proliferation, transposition and selection of a 20-kilobase (kb) duplicated segment throughout 15 Mb of the short arm of human chromosome 16. The dispersal of this segment was accompanied by considerable variation in chromosomal-map location and copy number among hominoid species. In humans, we identified a gene family (morpheus) within the duplicated segment. Comparison of putative protein-encoding exons revealed the most extreme case of positive selection among hominoids. The major episode of enhanced amino-acid replacement occurred after the separation of human and great-ape lineages from the orangutan. Positive selection continued to alter amino-acid composition after the divergence of human and chimpanzee lineages. The rapidity and bias for amino-acid-altering nucleotide changes suggest adaptive evolution of the morpheus gene family during the emergence of humans and African apes. Moreover, some genes emerge and evolve very rapidly, generating copies that bear little similarity to their ancestral precursors. Consequently, a small fraction of human genes may not possess discernible orthologues within the genomes of model organisms.     

S-nitrosothiols signal the ventilatory response to hypoxia

Increased ventilation in response to hypoxia has been appreciated for over a century, but the biochemistry underlying this response remains poorly understood. Here we define a pathway in which increased minute ventilation (&Vdot;E ) is signalled by deoxyhaemoglobin-derived S-nitrosothiols (SNOs). Specifically, we demonstrate that S-nitrosocysteinyl glycine (CGSNO) and S-nitroso-l-cysteine (l-CSNO)-but not S-nitroso-d-cysteine (d-CSNO)-reproduce the ventilatory effects of hypoxia at the level of the nucleus tractus solitarius (NTS). We show that plasma from deoxygenated, but not from oxygenated, blood produces the ventilatory effect of both SNOs and hypoxia. Further, this activity is mediated by S-nitrosoglutathione (GSNO), and GSNO activation by gamma-glutamyl transpeptidase (gamma-GT) is required. The normal response to hypoxia is impaired in a knockout mouse lacking gamma-GT. These observations suggest that S-nitrosothiol biochemistry is of central importance to the regulation of breathing.     

Feeding by the Great Basin spadefoot toad ( Spea intermontana ) (Anura: Pelobatidae)

The present study analyzed the stomach contents of 65 Great Basin spadefoot toads, Spea intermontana (Cope), collected in an area of irrigation runoff in south central Washington State. Toads were collected by pitfall trapping. Traps were maintained for 1 year beginning in April 2002. Toads consumed at least 56 different arthropod taxa belonging to the orders Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera, Neuroptera, Orthoptera, Trichoptera, Collembola, and Araneae. Ants and darkling beetles were among the most common prey. Feeding appeared to be very generalized with the toads accepting almost anything they could capture and subdue.     

Estimating root biomass and distribution after fire in a Great Basin woodland using cores and pits

Quantifying root biomass is critical to an estimation and understanding of ecosystem net primary production, biomass partitioning, and belowground competition. We compared 2 methods for determining root biomass: a new soil-coring technique and traditional excavation of quantitative pits. We conducted the study in an existing Joint Fire Sciences demonstration area in the central Great Basin. This area is representative of a shrub (sagebrush) ecosystem exhibiting tree (pinyon and juniper) encroachment. The demonstration area had a prescribed burn implemented 4 years prior to our study, and we sampled both control and burned plots. The samples were stratified across 3 microsites (interspace, under shrub, and under tree) and 4 soil depths (0–8, 8–23, 23–38, and 38–52 cm) to determine the effects of plant life form and burning on root biomass. We found that estimates of total root biomass were similar between quantitative pits and our soil cores. However, cores tended to show a more even distribution of root biomass across all microsites and depths than did pits. Overall, results indicated that root biomass differs significantly among microsites and soil depths and that the amount of root biomass at a given depth differs among microsites. Burning reduced root biomass in our study by 23% and altered the spatial distribution of root mass.     

Survey indicators for pygmy rabbits: temporal trends of burrow systems and pellets

Obtaining estimates of absolute abundance for rare or cryptic species can be challenging. In these cases,methods using indirect indicators such as sign might offer useful indices of population size. Pygmy rabbits ( Brachylagus idahoensis ) are small, burrowing lagomorphs for which methods for population assessment and monitoring are needed. Current tools for estimating relative abundance rely on detecting and assessing fecal pellets and burrow systems. We evaluated temporal changes in each of these indicators to gauge their potential usefulness as indicators of relative and absolute abundance of pygmy rabbits. Pellet persistence was strongly influenced by environmental exposure, and based on our data, we estimated that maximum persistence of fecal pellets would be 24–34 months. Pellet appearance (color) was affected by both time and exposure. Burrow systems were remarkably resilient over the course of the study. Probability of burrow systems transitioning between activity classes (active, recent, and old) did not vary detectably by study site, season, or year. We suggest that 2 protocols currently used for classification of pygmy rabbit burrow systems are most useful for different applications. Further work is needed, however, to link such assessments to quantitative estimates of population size.