Evidence of viral adaptation to HLA class I-restricted immune pressure in chronic hepatitis C virus infection

Cellular immune responses are an important correlate of hepatitis C virus (HCV) infection outcome. These responses are governed by the host's human leukocyte antigen (HLA) type, and HLA-restricted viral escape mutants are a critical aspect of this host-virus interaction. We examined the driving forces of HCV evolution by characterizing the in vivo selective pressure(s) exerted on single amino acid residues within nonstructural protein 3 (NS3) by the HLA types present in two host populations. Associations between polymorphisms within NS3 and HLA class I alleles were assessed in 118 individuals from Western Australia and Switzerland with chronic hepatitis C infection, of whom 82 (69%) were coinfected with human immunodeficiency virus. The levels and locations of amino acid polymorphisms exhibited within NS3 were remarkably similar between the two cohorts and revealed regions under functional constraint and selective pressures. We identified specific HCV mutations within and flanking published epitopes with the correct HLA restriction and predicted escaped amino acid. Additional HLA-restricted mutations were identified that mark putative epitopes targeted by cell-mediated immune responses. This analysis of host-virus interaction reveals evidence of HCV adaptation to HLA class I-restricted immune pressure and identifies in vivo targets of cellular immune responses at the population level.

Diagnostic significance of Neospora caninum DNA detected by PCR in cattle serum

A nested PCR that successfully detected Neospora caninum DNA in serum of cattle was used for investigation of selected abortion cases and in a study of healthy pregnant cows at an abattoir. N. caninum DNA was not detected in serum from antibody positive dams that aborted due to N. caninum, but was present in serum of some antibody negative dams that aborted due to other causes. N. caninum DNA was also found in the serum of about half of the animals that aborted of undetermined cause, but was not detected in cow sera from two beef cattle herds in Western Australia with no recent history of abortion. In the abattoir study of 79 dams and their foetuses N. caninum DNA was found in serum of 3 dams and in material from 11 foetuses. The majority of the cows and all foetuses were antibody negative. Our findings suggest that there is no obvious relationship between the presence or absence of N. caninum DNA in serum and the presence of antibodies to N. caninum in dams, the presence of N. caninum DNA in foetuses or abortion due to N. caninum. This is the first report of the detection of N. caninum DNA in serum of cattle rather than the white blood cell fraction. It indicates the presence of free tachyzoites and/or parasite DNA in circulation. The results suggest that persistent infection in the absence of antibodies is a possible outcome of N. caninum infection. Infection of foetuses in the absence of antibodies supports the possibility of persistent infection due to immunotolerance to an early in utero infection. It is therefore important to test for N. caninum DNA as well as antibodies for the detection of exposed and/or infected animals. However, the presence or absence of N. caninum antibodies or DNA did not support nor exclude N. caninum as the cause of abortion. Additional criteria are required for a positive diagnosis of abortion caused by N. caninum.

The new Australasian goblin spider genus Prethopalpus (Araneae, Oonopidae)

The new goblin spider genus Prethopalpus is restricted to the Australasian tropics, from the lower Himalayan Mountains in Nepal and India to the Malaysian Peninsula, Indonesia, Papua New Guinea, and Australia. Prethopalpus contains those species with a swollen palpal patella, which is one to two times the size of the femur, together with a cymbium and bulb that is usually separated, although it is largely fused in four species. The type species Opopaea fosuma Burger et al. from Sumatra, and Camptoscaphiella infernalis Harvey and Edward from Western Australia are newly transferred to Prethopalpus. The genus consists of 41 species of which 39 are newly described: P. ilam Baehr (♂, ♀) from Nepal; P. khasi Baehr (♂), P. madurai Baehr (♂), P. mahanadi Baehr (♂, ♀), and P. meghalaya Baehr (♂, ♀) from India; P. bali Baehr (♂), P. bellicosus Baehr and Thoma (♂, ♀), P. brunei Baehr (♂, ♀), P. deelemanae Baehr and Thoma (♂), P. java Baehr (♂, ♀), P. kranzae Baehr (♂), P. kropfi Baehr (♂, ♀), P. leuser Baehr (♂, ♀), P. magnocularis Baehr and Thoma (♂), P. pahang Baehr (♂), P. perak Baehr (♂, ♀), P. sabah Baehr (♂, ♀), P. sarawak Baehr (♂), P. schwendingeri Baehr (♂, ♀), and P. utara Baehr (♂, ♀) from Indonesia and Malaysia; and P. alexanderi Baehr and Harvey (♂), P. attenboroughi Baehr and Harvey (♂), P. blosfeldsorum Baehr and Harvey (♂), P. boltoni Baehr and Harvey (♂, ♀), P. callani Baehr and Harvey (♂, ♀), P. cooperi Baehr and Harvey (♂), P. eberhardi Baehr and Harvey (♂, ♀), P. framenaui Baehr and Harvey (♂, ♀), P. humphreysi Baehr and Harvey (♂, ♀), P. kintyre Baehr and Harvey (♂), P. scanloni Baehr and Harvey (♂), P. pearsoni Baehr and Harvey (♂), P. julianneae Baehr and Harvey (♂), P. maini Baehr and Harvey (♂, ♀), P. marionae Baehr and Harvey (♂, ♀), P. platnicki Baehr and Harvey (♂, ♀), P. oneillae Baehr and Harvey (♂), P. rawlinsoni Baehr and Harvey (♂), and P. tropicus Baehr and Harvey (♂, ♀) from Australia and Papua New Guinea. Three separate keys to species from different geographical regions are provided. Most species are recorded from single locations and only three species are more widely distributed. A significant radiation of blind troglobites comprising 14 species living in subterranean ecosystems in Western Australia is discussed. These include several species that lack abdominal scuta, a feature previously used to define subfamilies of Oonopidae.

The Crystal Chemistry of Holtite

Holtite, approximately (Al,Ta,square)Al(6)(BO(3))(Si,Sb(3+),As(3+))(Sigma 3)O(12)(O,OH,square)(Sigma 3), is a member of the dumortierite group that has been found in pegmatite, or alluvial deposits derived from pegmatite, at three localities: Greenbushes, Western Australia; Voron'i Tundry, Kola Peninsula, Russia; and Szklary, Lower Silesia, Poland. Holtite can contain >30 wt.% Sb(2)O(3), As(2)O(3), Ta(2)O(5), Nb(2)O(5), and TiO(2) (taken together), but none of these constituents is dominant at a crystallographic site, which raises the question whether this mineral is distinct from dumortierite. The crystal structures of four samples from the three localities have been refined to R(1) = 0.02-0.05. The results show dominantly: Al, Ta, and vacancies at the Al(1) position; Al and vacancies at the Al(2), (3) and (4) sites; Si and vacancies at the Si positions; and Sb, As and vacancies at the Sb sites for both Sb-poor (holtite I) and Sb-rich (holtite II) specimens. Although charge-balance calculations based on our single-crystal structure refinements suggest that essentially no water is present, Fourier transform infrared spectra confirm that some OH is present in the three samples that could be measured. By analogy with dumortierite, the largest peak at 3505-3490 cm(-1) is identified with OH at the O(2) and O(7) positions. The single-crystal X-ray refinements and FTIR results suggest the following general formula for holtite: Al(7-[5x+y+z]/3)(Ta,Nb)(x)square([2x+y+z]/3)BSi(3-y)(Sb,As)(y)O(18-y-z)(OH)(z), where x is the total number of pentavalent cations, y is the total amount of Sb + As, and z <= y is the total amount of OH. Comparison with the electron microprobe compositions suggests the following approximate general formulae Al(5.83)(Ta,Nb)(0.50)square(0.67)BSi(2.50)(Sb,As)(0.50)O(17.00)(OH)(0.50) and Al(5.92)(Ta,Nb)(0.25)square(0.83)BSi(2.00)(Sb,As)(1.00) O(16.00)(OH)(1.00) for holtite I and holtite II respectively. However, the crystal structure refinements do not indicate a fundamental difference in cation ordering that might serve as a criterion for recognizing the two holtites as distinct species, and anion compositions are also not sufficiently different. Moreover, available analyses suggest the possibility of a continuum in the Si/(Sb + As) ratio between holtite I and dumortierite, and at least a partial continuum between holtite I and holtite II. We recommend that use of the terms holtite I and holtite II be discontinued.

Major and trace element analyses of ODP Leg 120 volcanic rocks (Table 1)

Widespread Lower Cretaceous magmatism occurred along the Indian-Australian/Antarctic margins, and in the juvenile Indian Ocean, during the rifting of eastern Gondwana. The formation of this magmatic province probably began around 120-130 Ma with the eruption of basalts on the Naturaliste Plateau and at Bunbury, western Australia. On the northeast margin of India, activity began around 117 Ma with the Rajmahal continental basalts and associated lamprophyre intrusions. The formation of the Kerguelen Plateau in the Indian Ocean began no later than 114 Ma. Ultramafic lamprophyres (alnoites) were emplaced in the Prince Charles Mountains near the Antarctic continental margin at ~ 110 Ma. These events are considered to be related to a major mantle plume, the remnant of which is situated beneath the region of Kerguelen and Heard islands at the present day. Geochemical data are presented for each of these volcanic suites and are indicative of complex interactions between asthenosphere-derived magmas and the continental lithosphere. Kerguelen Plateau basalts have Sr and Nd isotopic compositions lying outside the field for Indian Ocean mid-ocean ridge basalts (MORB) but, with the exception of Site 738 at the southern end of the plateau, within the range of more recent hotspot basalts from Kerguelen and Heard Islands. However, a number of the plateau tholeiites are characterized by lower 206Pb/204Pb ratios than are basalts from Kerguelen Island, and many also have anomalously high La/Nb ratios. These features suggest that the source of the Kerguelen Plateau basalts suffered contamination by components derived from the Gondwana continental lithosphere. An extreme expression of this lithospheric signature is shown by a tholeiite from Site 738, suggesting that the southernmost part of the Kerguelen Plateau may be underlain by continental crust. The Rajmahal tholeiites mostly fall into two distinct geochemical groups. Some Group I tholeiites have Sr and Nd isotopic compositions and incompatible element abundances, similar to Kerguelen Plateau tholeiites from Sites 749 and 750, indicating that the Kerguelen-Heard mantle plume may have directly furnished Rajmahal volcanism. However, their elevated 207Pb/204Pb ratios indicate that these magmas did not totally escape contamination by continental lithosphere. In contrast to the Group I tholeiites, significant contamination is suggested for Group II Rajmahal tholeiites, on the basis of incompatible element abundances and isotopic compositions. The Naturaliste Plateau and the Bunbury Basalt samples show varying degrees of enrichment in incompatible elements over normal MORB. The Naturaliste Plateau samples (and Bunbury Basalt) have high La/Nb ratios, a feature not inconsistent with the notion that the plateau may consist of stretched continental lithosphere, near the ocean-continent divide.