Tumour-derived soluble MIC ligands impair expression of NKG2D and T-cell activation

Engagement of the NKG2D receptor by tumour-associated ligands may promote tumour rejection by stimulating innate and adaptive lymphocyte responses. In humans, NKG2D is expressed on most natural killer cells, gammadelta T cells and CD8alphabeta T cells. Ligands of NKG2D include the major histocompatibility complex class I homologues MICA and MICB, which function as signals of cellular stress. These molecules are absent from most cells and tissues but can be induced by viral and bacterial infections and are frequently expressed in epithelial tumours. MIC engagement of NKG2D triggers natural killer cells and costimulates antigen-specific effector T cells. Here we show that binding of MIC induces endocytosis and degradation of NKG2D. Expression of NKG2D is reduced markedly on large numbers of tumour-infiltrating and matched peripheral blood T cells from individuals with cancer. This systemic deficiency is associated with circulating tumour-derived soluble MICA, causing the downregulation of NKG2D and in turn severe impairment of the responsiveness of tumour-antigen-specific effector T cells. This mode of T-cell silencing may promote tumour immune evasion and, by inference, compromise host resistance to infections.     

Fire-induced erosion and millennial-scale climate change in northern ponderosa pine forests

Western US ponderosa pine forests have recently suffered extensive stand-replacing fires followed by hillslope erosion and sedimentation. These fires are usually attributed to increased stand density as a result of fire suppression, grazing and other land use, and are often considered uncharacteristic or unprecedented. Tree-ring records from the past 500 years indicate that before Euro-American settlement, frequent, low-severity fires maintained open stands. However, the pre-settlement period between about ad 1500 and ad 1900 was also generally colder than present, raising the possibility that rapid twentieth-century warming promoted recent catastrophic fires. Here we date fire-related sediment deposits in alluvial fans in central Idaho to reconstruct Holocene fire history in xeric ponderosa pine forests and examine links to climate. We find that colder periods experienced frequent low-severity fires, probably fuelled by increased understory growth. Warmer periods experienced severe droughts, stand-replacing fires and large debris-flow events that comprise a large component of long-term erosion and coincide with similar events in sub-alpine forests of Yellowstone National Park. Our results suggest that given the powerful influence of climate, restoration of processes typical of pre-settlement times may be difficult in a warmer future that promotes severe fires.     

Role of a free-living amoeba from water, Acanthamoaba castellani, in the transport of naked or enveloped animal viruses

The trophozo?ts of Acanthamoeba castellanii are unable to adsorb poliovirus or vesicular stomatitis Virus. After encystment in medium containing respectively 5.4 x 10(8) and 3 x 10(9) P.F.U./ml cysts did not contain Viruses. These data do not agree with a current hypothesis by which water's free Amoeba could carry animal Viruses.     

Tumour evolution inferred by single-cell sequencing

Genomic analysis provides insights into the role of copy number variation in disease, but most methods are not designed to resolve mixed populations of cells. In tumours, where genetic heterogeneity is common, very important information may be lost that would be useful for reconstructing evolutionary history. Here we show that with flow-sorted nuclei, whole genome amplification and next generation sequencing we can accurately quantify genomic copy number within an individual nucleus. We apply single-nucleus sequencing to investigate tumour population structure and evolution in two human breast cancer cases. Analysis of 100 single cells from a polygenomic tumour revealed three distinct clonal subpopulations that probably represent sequential clonal expansions. Additional analysis of 100 single cells from a monogenomic primary tumour and its liver metastasis indicated that a single clonal expansion formed the primary tumour and seeded the metastasis. In both primary tumours, we also identified an unexpectedly abundant subpopulation of genetically diverse 'pseudodiploid' cells that do not travel to the metastatic site. In contrast to gradual models of tumour progression, our data indicate that tumours grow by punctuated clonal expansions with few persistent intermediates.     

Chemical remodelling of cell surfaces in living animals

Cell surfaces are endowed with biological functionality designed to mediate extracellular communication. The cell-surface repertoire can be expanded to include abiotic functionality through the biosynthetic introduction of unnatural sugars into cellular glycans, a process termed metabolic oligosaccharide engineering. This technique has been exploited in fundamental studies of glycan-dependent cell-cell and virus-cell interactions and also provides an avenue for the chemical remodelling of living cells. Unique chemical functional groups can be delivered to cell-surface glycans by metabolism of the corresponding unnatural precursor sugars. These functional groups can then undergo covalent reaction with exogenous agents bearing complementary functionality. The exquisite chemical selectivity required of this process is supplied by the Staudinger ligation of azides and phosphines, a reaction that has been performed on cultured cells without detriment to their physiology. Here we demonstrate that the Staudinger ligation can be executed in living animals, enabling the chemical modification of cells within their native environment. The ability to tag cell-surface glycans in vivo may enable therapeutic targeting and non-invasive imaging of changes in glycosylation during disease progression.     

Changes in carbon dioxide during an oceanic anoxic event linked to intrusion into Gondwana coals

The marine sedimentary record exhibits evidence for episodes of enhanced organic carbon burial known as 'oceanic anoxic events' (OAEs). They are characterized by carbon-isotope excursions in marine and terrestrial reservoirs and mass extinction of marine faunas. Causal mechanisms for the enhancement of organic carbon burial during OAEs are still debated, but it is thought that such events should draw down significant quantities of atmospheric carbon dioxide. In the case of the Toarcian OAE (approximately 183 million years ago), a short-lived negative carbon-isotope excursion in oceanic and terrestrial reservoirs has been interpreted to indicate raised atmospheric carbon dioxide caused by oxidation of methane catastrophically released from either marine gas hydrates or magma-intruded organic-rich rocks. Here we test these two leading hypotheses for a negative carbon isotopic excursion marking the initiation of the Toarcian OAE using a high-resolution atmospheric carbon dioxide record obtained from fossil leaf stomatal frequency. We find that coincident with the negative carbon-isotope excursion carbon dioxide is first drawn down by 350 +/- 100 p.p.m.v. and then abruptly elevated by 1,200 +/- 400 p.p.m.v, and infer a global cooling and greenhouse warming of 2.5 +/- 0.1 degrees C and 6.5 +/- 1 degrees C, respectively. The pattern and magnitude of carbon dioxide change are difficult to reconcile with catastrophic input of isotopically light methane from hydrates as the cause of the negative isotopic signal. Our carbon dioxide record better supports a magma-intrusion hypothesis, and suggests that injection of isotopically light carbon from the release of thermogenic methane occurred owing to the intrusion of Gondwana coals by Toarcian-aged Karoo-Ferrar dolerites.     

Analysis of the DNA sequence and duplication history of human chromosome 15

Here we present a finished sequence of human chromosome 15, together with a high-quality gene catalogue. As chromosome 15 is one of seven human chromosomes with a high rate of segmental duplication, we have carried out a detailed analysis of the duplication structure of the chromosome. Segmental duplications in chromosome 15 are largely clustered in two regions, on proximal and distal 15q; the proximal region is notable because recombination among the segmental duplications can result in deletions causing Prader-Willi and Angelman syndromes. Sequence analysis shows that the proximal and distal regions of 15q share extensive ancient similarity. Using a simple approach, we have been able to reconstruct many of the events by which the current duplication structure arose. We find that most of the intrachromosomal duplications seem to share a common ancestry. Finally, we demonstrate that some remaining gaps in the genome sequence are probably due to structural polymorphisms between haplotypes; this may explain a significant fraction of the gaps remaining in the human genome.