Selection pressure-driven evolution of the Epstein-Barr virus-encoded oncogene LMP1 in virus isolates from southeast Asia

The geographically constrained distribution of Epstein-Barr virus (EBV)-associated nasopharyngeal carcinoma (NPC) in southeast Asian populations suggests that both viral and host genetics may influence disease risk. Although susceptibility loci have been mapped within the human genome, the role of viral genetics in the focal distribution of NPC remains an enigma. Here we report a molecular phylogenetic analysis of an NPC-associated viral oncogene, LMP1, in a large panel of EBV isolates from southeast Asia and from Papua New Guinea, Africa, and Australia, regions of the world where NPC is and is not endemic, respectively. This analysis revealed that LMP1 sequences show a distinct geographic structure, indicating that the southeast Asian isolates have evolved as a lineage distinct from those of Papua New Guinea, African, and Australian isolates. Furthermore, a likelihood ratio test revealed that the C termini of the LMP1 sequences of the southeast Asian lineage are under significant positive selection pressure, particularly at some sites within the C-terminal activator regions. We also present evidence that although the N terminus and transmembrane region of LMP1 have undergone recombination, the C-terminal region of the gene has evolved without any history of recombination. Based on these observations, we speculate that selection pressure may be driving the LMP1 sequences in virus isolates from southeast Asia towards a more malignant phenotype, thereby influencing the endemic distribution of NPC in this region.

A refined solution to Earth's hidden niobium: implications for evolution of continental crust and mode of core formation

New high-precision niobium (Nb) and tantalum (Ta) concentration data are presented for early Archaean metabasalts, metabasaltic komatiites and their erosion products (mafic metapelites) from SW Greenland and the Acasta gneiss complex, Canada. Individual datasets consistently show sub-chondritic Nb/Ta ratios averaging 15.1+/-11.6. This finding is discussed with regard to two competing models for the solution of the Nb-deficit that characterises the accessible Earth. Firstly, we test whether Nb could have sequestered into the core due to its slightly siderophile (or chalcophile) character under very reducing conditions, as recently proposed from experimental evidence. We demonstrate that troilite inclusions of the Canyon Diablo iron meteorite have Nb and V concentrations in excess of typical chondrites but that the metal phase of the Grant, Toluca and Canyon Diablo iron meteorites do not have significant concentrations of these lithophile elements. We find that if the entire accessible Earth Nb-deficit were explained by Nb in the core, only ca. 17% of the mantle could be depleted and that by 3.7 Ga, continental crust would have already achieved ca. 50% of its present mass. Nb/Ta systematics of late Archaean metabasalts compiled from the literature would further require that by 2.5 Ga, 90% of the present mass of continental crust was already in existence. As an alternative to this explanation, we propose that the average Nb/Ta ratio (15.1+/-11.6) of Earth's oldest mafic rocks is a valid approximation for bulk silicate Earth. This would require that ca. 13% of the terrestrial Nb resided in the Ta-free core. Since the partitioning of Nb between silicate and metal melts depends largely on oxygen fugacity and pressure, this finding could mean that metal/silicate segregation did not occur at the base of a deep magma ocean or that the early mantle was slightly less reducing than generally assumed. A bulk silicate Earth Nb/Ta ratio of 15.1 allows for depletion of up to 40% of the total mantle. This could indicate that in addition to the upper mantle, a portion of the lower mantle is depleted also, or if only the upper mantle were depleted, an additional hidden high Nb/Ta reservoir must exist. Comparison of Nb/Ta systematics between early and late Archaean metabasalts supports the latter idea and indicates deeply subducted high Nb/Ta eclogite slabs could reside in the mantle transition zone or the lower mantle. Accumulation of such slabs appears to have commenced between 2.5 and 2.0 Ga. Regardless of these complexities of terrestrial Nb/Ta systematics, it is shown that the depleted mantle Nb/Th ratio is a very robust proxy for the amount of extracted continental crust, because the temporal evolution of this ratio is dominated by Th-loss to the continents and not Nb-retention in the mantle. We present a new parameterisation of the continental crust volume versus age curve that specifically explores the possibility of lithophile element loss to the core and storage of eclogite slabs in the transition zone. (C) 2003 Elsevier Science B.V. All rights reserved.

When vicars meet: A narrow contact zone between morphologically cryptic phylogeographic lineages of the rainforest skink, Carlia rubrigularis

Phylogeographic analyses of the fauna of the Australian wet tropics rainforest have provided strong evidence for long-term isolation of populations among allopatric refugia, yet typically there is no corresponding divergence in morphology. This system provides an opportunity to examine the consequences of geographic isolation, independent of morphological divergence, and thus to assess the broader significance of historical subdivisions revealed through mitochondrial DNA phylogeography. We have located and characterized a zone of secondary contact between two long isolated (mtDNA divergence > 15%) lineages of the skink Carlia rubrigularis using one mitochondrial and eight nuclear (two intron, six microsatellite) markers. This revealed a remarkably narrow (width < 3 km) hybrid zone with substantial linkage disequilibrium and strong deficits of heterozygotes at two of three nuclear loci with diagnostic alleles. Cline centers were coincident across loci. Using a novel form of likelihood analysis, we were unable to distinguish between sigmoidal and stepped cline shapes except at one nuclear locus for which the latter was inferred. Given estimated dispersal rates of 90-133 m x gen(-1/2) and assuming equilibrium, the observed cline widths suggest effective selection against heterozygotes of at least 22-49% and possibly as high as 70%. These observations reveal substantial postmating isolation, although the absence of consistent deviations from Hardy-Weinberg equilibrium at diagnostic loci suggests that there is little accompanying premating isolation. The tight geographic correspondence between transitions in mtDNA and those for nuclear genes and corresponding evidence for selection against hybrids indicates that these morphologically cryptic phylogroups could be considered as incipient species. Nonetheless, we caution against the use of mtDNA phylogeography as a sole criterion for defining species boundaries.

Evidence for endothermic ancestors of crocodiles at the stem of archosaur evolution

Physiological, anatomical, and developmental features of the crocodilian heart support the paleontological evidence that the ancestors of living crocodilians were active and endothermic, but the lineage reverted to ectothermy when it invaded the aquatic, ambush predator niche. In endotherms, there is a functional nexus between high metabolic rates, high blood flow rates, and complete separation of high systemic blood pressure from low pulmonary blood pressure in a four-chambered heart. Ectotherms generally lack all of these characteristics, but crocodilians retain a four-chambered heart. However, crocodilians have a neurally controlled, pulmonary bypass shunt that is functional in diving. Shunting occurs outside of the heart and involves the left aortic arch that originates from the right ventricle, the foramen of Panizza between the left and right aortic arches, and the cog-tooth valve at the base of the pulmonary artery. Developmental studies show that all of these uniquely crocodilian features are secondarily derived, indicating a shift from the complete separation of blood flow of endotherms to the controlled shunting of ectotherms. We present other evidence for endothermy in stem archosaurs and suggest that some dinosaurs may have inherited the trait.

Exploratory modelling of grinding pressure within a compressed particle bed

With increasing industry interest in high pressure roll grinding (HPGR) technology, there is a strong incentive for improved understanding of the nature of grinding pressure that exists in the interior of a compressed particle bed. This corresponds to the crushing region of the HPGR. The relationship between applied pressure (stress) to the particle bed and induced pressure (stress) within particles and at contact points between particles is of particular interest. A detailed parametric investigation is beyond the scope of this exploratory paper. However, this exploratory investigation does suggest some interesting behaviour. The compressed particle bed within an 80 turn diameter piston has been modelled using Particle Flow Code for three dimensions. PFC3D is a discrete element code. The total number of simulated particles was 1225 and 2450 for two beds of different thickness. Particle diameters were uniformly distributed between 4 and 4.5 mm. The results of the simulations show that stress intensity within the simulated particle beds and within the observed particles increased with increase of the applied stress. The intensity of the average vertical stress in the selected particles tended to be comparable with the intensity of the pressure applied to the surface of particle bed and was only occasionally higher. However, the stress at contact points between particles could be several times higher. In a real crusher, such high stress amplification at contacts will quickly decrease due to local crushing and a resultant increase the size of the contact area. Therefore, its significance is likely to be relatively small in an industrial context. The modelling results also suggest that failure within the particle bed will progress from the crushing surface towards the depth of the bed. (c) 2006 Elsevier Ltd. All rights reserved.

Experimental and analytical study of the effect of contact angle on liquid convective heat transfer in microchannels

In this paper we examine the effect of contact angle (or surface wettability) on the convective heat transfer coefficient in microchannels. Slip flow, where the fluid velocity at the wall is non-zero, is most likely to occur in microchannels due to its dependence on shear rate or wall shear stress. We show analytically that for a constant pressure drop, the presence of slip increases the Nusselt number. In a microchannel heat exchanger we modified the surface wettability from a contact angle of 20 degrees-120 degrees using thin film coating technology. Apparent slip flow is implied from pressure and flow rate measurements with a departure from classical laminar friction coefficients above a critical shear rate of approximately 10,000 s(-1). The magnitude of this departure is dependant on the contact angle with higher contact angles surfaces exhibiting larger pressure drop decreases. Similarly, the non-dimensional heat flux is found to decrease relative to laminar non-slip theory, and this decrease is also a function of the contact angle. Depending on the contact angle and the wall shear rate, variations in the heat transfer rate exceeding 10% can be expected. Thus the contact angle is an important consideration in the design of micro, and even more so, nano heat exchangers. (c) 2006 Elsevier Ltd. All rights reserved.

Speech production in Parkinson's disease: I. An electropalatographic investigation of tongue-palate contact patterns

Previous studies have indicated that consonant imprecision in Parkinson's disease (PD) may result from a reduction in the amplitude of lingual movements or articulatory undershoot. While this has been postulated, direct measurement of the tongue's contact with the hard palate during speech production has not been undertaken. Therefore, the present study aimed to use electropalatography (EPG) to determine the exact nature of tongue-palate contact in a group of individuals with PD and consonant imprecision (n=9). Furthermore, the current investigation also aimed to compare the results of the participants with PD to a group of aged (n=7) and young (n=8) control speakers to determine the relative contribution of ageing of the lingual musculature to any articulatory deficits noted. Participants were required to read aloud the phrase 'I saw a ___ today' with the artificial palate in-situ. Target words included the consonants /l/, /s/ and /t/ in initial position in both the /i/ and /a/ vowel environments. Phonetic transcription of phoneme productions and description of error types was completed. Furthermore, representative frames of contact were employed to describe the features of tongue-palate contact and to calculate spatial palatal indices. Results of the perceptual investigation revealed that perceived undershooting of articulatory targets distinguished the participant group with PD from the control groups. However, objective EPG assessment indicated that undershooting of the target consonant was not the cause of the perceived articulatory errors. It is, therefore, possible that reduced pressure of tongue contact with the hard palate, sub-lingual deficits or impaired articulatory timing resulted in the perceived undershooting of the target consonants.

Noise in detection of qubit states using a quantum point contact

We present a model for detection of the states of a coupled quantum dots (qubit) by a quantum point contact. Most proposals for measurements of states of quantum systems are idealized. However in a real laboratory the measurements cannot be perfect due to practical devices and circuits. The models using ideal devices are not sufficient for describing the detection information of the states of the quantum systems. Our model therefore includes the extension to a non-ideal measurement device case using an equivalent circuit. We derive a quantum trajectory that describes the stochastic evolution of the state of the system of the qubit and the measuring device. We calculate the noise power spectrum of tunnelling events in an ideal and a non-ideal quantum point contact measurement respectively. We found that, for the strong coupling case it is difficult to obtain information of the quantum processes in the qubit by measurements using a non-ideal quantum point contact. The noise spectra can also be used to estimate the limits of applicability of the ideal model.