Recommendations of the 2006 Human Variome Project meeting

Lists of variations in genomic DNA and their effects have been kept for some time and have been used in diagnostics and research. Although these lists have been carefully gathered and curated, there has been little standardization and coordination, complicating their use. Given the myriad possible variations in the estimated 24,000 genes in the human genome, it would be useful to have standard criteria for databases of variation. Incomplete collection and ascertainment of variants demonstrates a need for a universally accessible system. These and other problems led to the World Heath Organization-cosponsored meeting on June 20-23, 2006 in Melbourne, Australia, which launched the Human Variome Project. This meeting addressed all areas of human genetics relevant to collection of information on variation and its effects. Members of each of eight sessions (the clinic and phenotype, the diagnostic laboratory, the research laboratory, curation and collection, informatics, relevance to the emerging world, integration and federation and funding and sustainability) developed a number of recommendations that were then organized into a total of 96 recommendations to act as a foundation for future work worldwide. Here we summarize the background of the project, the meeting and its recommendations.     

Functional significance of the Kunitz-type inhibitory domains of lipoprotein-associated coagulation inhibitor

Blood coagulation can be initiated when factor VII or VIIa, a plasma protease, binds to its essential cofactor, tissue factor (TF), and proteolytically activates factors IX and X, triggering a cascade of events which eventually leads to the formation of thrombin and a fibrin clot. Plasma contains a lipoprotein-associated coagulation inhibitor (LACI) which inhibits activated factor X (Xa) directly and, in a Xa-dependent way, inhibits VII(a)/TF activity, presumably by forming a quaternary Xa/LACI/VII(a)/TF complex. Sequence analysis of complementary DNA clones has shown that LACI contains three tandemly repeated Kunitz-type serine protease inhibitory domains. To investigate the relationship between these Kunitz structures and LACI function, we have used site-directed mutagenesis to produce altered forms of LACI in which the residue at the active-site cleft of each Kunitz domain has been individually changed. The second Kunitz domain is required for efficient binding and inhibition of Xa, and both Kunitz domains 1 and 2 are required for the inhibition of VIIa/TF activity; but alteration of the active-site residue of the third Kunitz domain has no significant effect on either function. We propose that in the putative inhibitory complex, Kunitz domain 1 is bound to the active site of VII(a)/TF and that Kunitz domain 2 is bound to Xa's active site.     

Protective action of irradiated bone marrow cells

Zusammenfassung Wurdein vitro röntgenbestrahltes Knochenmark (475r, 950 r, 1425 r) in letal bestrahlte Mäuse (LD 100/11=950 r) injiziert, so ergab sich: Isologes Knochenmark, mit 950 r bestrahlt, besitzt noch beachtliche Schutzwirkung; bestrahltes homologes und heterologes Knochenmark war weniger oder ganz inaktiv.     

Structural and temporal requirements for geomagnetic field reversal deduced from lava flows

Reversals of the Earth's magnetic field reflect changes in the geodynamo--flow within the outer core--that generates the field. Constraining core processes or mantle properties that induce or modulate reversals requires knowing the timing and morphology of field changes that precede and accompany these reversals. But the short duration of transitional field states and fragmentary nature of even the best palaeomagnetic records make it difficult to provide a timeline for the reversal process. 40Ar/39Ar dating of lavas on Tahiti, long thought to record the primary part of the most recent 'Matuyama-Brunhes' reversal, gives an age of 795 +/- 7 kyr, indistinguishable from that of lavas in Chile and La Palma that record a transition in the Earth's magnetic field, but older than the accepted age for the reversal. Only the 'transitional' lavas on Maui and one from La Palma (dated at 776 +/- 2 kyr), agree with the astronomical age for the reversal. Here we propose that the older lavas record the onset of a geodynamo process, which only on occasion would result in polarity change. This initial instability, associated with the first of two decreases in field intensity, began approximately 18 kyr before the actual polarity switch. These data support the claim that complete reversals require a significant period for magnetic flux to escape from the solid inner core and sufficiently weaken its stabilizing effect.     

Dental microwear texture analysis shows within-species diet variability in fossil hominins

Reconstructing the diets of extinct hominins is essential to understanding the paleobiology and evolutionary history of our lineage. Dental microwear, the study of microscopic tooth-wear resulting from use, provides direct evidence of what an individual ate in the past. Unfortunately, established methods of studying microwear are plagued with low repeatability and high observer error. Here we apply an objective, repeatable approach for studying three-dimensional microwear surface texture to extinct South African hominins. Scanning confocal microscopy together with scale-sensitive fractal analysis are used to characterize the complexity and anisotropy of microwear. Results for living primates show that this approach can distinguish among diets characterized by different fracture properties. When applied to hominins, microwear texture analysis indicates that Australopithecus africanus microwear is more anisotropic, but also more variable in anisotropy than Paranthropus robustus. This latter species has more complex microwear textures, but is also more variable in complexity than A. africanus. This suggests that A. africanus ate more tough foods and P. robustus consumed more hard and brittle items, but that both had variable and overlapping diets.     

No oceans on Titan from the absence of a near-infrared specular reflection

With its substantial atmosphere of nitrogen, hydrocarbons and nitriles, Saturn's moon Titan is a unique planetary satellite. Photochemical processing of the gaseous constituents produces an extended haze that obscures the surface. Soon after the Voyager fly-bys in 1980 and 1981 photochemical models led to the conclusion that there should be enough liquid methane/ethane/nitrogen to cover the surface to a depth of several hundred metres. Recent Earth-based radar echoes imply that surface liquid may be present at a significant fraction of the locations sampled. Here we present ground-based observations (at near-infrared wavelengths) and calculations showing that there is no evidence thus far for surface liquid. Combined with the specular signatures from radar observations, we infer mechanisms that produce very flat solid surfaces, involving a substance that was liquid in the past but is not in liquid form at the locations we studied.     

Young organic matter as a source of carbon dioxide outgassing from Amazonian rivers

Rivers are generally supersaturated with respect to carbon dioxide, resulting in large gas evasion fluxes that can be a significant component of regional net carbon budgets. Amazonian rivers were recently shown to outgas more than ten times the amount of carbon exported to the ocean in the form of total organic carbon or dissolved inorganic carbon. High carbon dioxide concentrations in rivers originate largely from in situ respiration of organic carbon, but little agreement exists about the sources or turnover times of this carbon. Here we present results of an extensive survey of the carbon isotope composition (13C and 14C) of dissolved inorganic carbon and three size-fractions of organic carbon across the Amazonian river system. We find that respiration of contemporary organic matter (less than five years old) originating on land and near rivers is the dominant source of excess carbon dioxide that drives outgassing in medium to large rivers, although we find that bulk organic carbon fractions transported by these rivers range from tens to thousands of years in age. We therefore suggest that a small, rapidly cycling pool of organic carbon is responsible for the large carbon fluxes from land to water to atmosphere in the humid tropics.     

Compositional maps of Saturn's moon Phoebe from imaging spectroscopy

The origin of Phoebe, which is the outermost large satellite of Saturn, is of particular interest because its inclined, retrograde orbit suggests that it was gravitationally captured by Saturn, having accreted outside the region of the solar nebula in which Saturn formed. By contrast, Saturn's regular satellites (with prograde, low-inclination, circular orbits) probably accreted within the sub-nebula in which Saturn itself formed. Here we report imaging spectroscopy of Phoebe resulting from the Cassini-Huygens spacecraft encounter on 11 June 2004. We mapped ferrous-iron-bearing minerals, bound water, trapped CO2, probable phyllosilicates, organics, nitriles and cyanide compounds. Detection of these compounds on Phoebe makes it one of the most compositionally diverse objects yet observed in our Solar System. It is likely that Phoebe's surface contains primitive materials from the outer Solar System, indicating a surface of cometary origin.