Changes in type‐specific human papillomavirus load predict progression to cervical cancer

Persistent high-risk human papillomavirus (HPV) infection is strongly associated with the development of high-grade cervical intraepithelial neoplasia or cancer (CIN3+). However, HPV infection is common and usually transient. Viral load measured at a single time-point is a poor predictor of the natural history of HPV infection. The profile of viral load evolution over time could distinguish HPV infections with carcinogenic potential from infections that regress. A case-cohort natural history study was set-up using a Belgian laboratory database processing more than 100,000 liquid cytology specimens annually. All cytology leftovers were submitted to real-time PCR testing identifying E6/E7 genes of 17 HPV types, with viral load expressed as HPV copies/cell. Samples from untreated women who developed CIN3+ (n = 138) and women with transient HPV infection (n = 601) who contributed at least three viral load measurements were studied. Only single-type HPV infections were selected. The changes in viral load over time were assessed by the linear regression slope for the productive and/or clearing phase of infection in women developing CIN3+ and women with transient infection respectively. Transient HPV infections generated similar increasing (0.21 copies/cell/day) and decreasing (−0.28 copies/cell/day) viral load slopes. In HPV infections leading to CIN3+, the viral load increased almost linearly with a slope of 0.0028 copies/cell/day. Difference in slopes between transient infections and infections leading to CIN3+ was highly significant (P < .0001). Serial type-specific viral load measurements predict the natural history of HPV infections and could be used to triage women in HPV-based cervical cancer screening.     

Manipulation of Auxin Transport in Plant Roots during Rhizobium Symbiosis and Nematode Parasitism

The plant rhizosphere harbors many different microorganisms, ranging from plant growth–promoting bacteria to devastating plant parasites. Some of these microbes are able to induce de novo organ formation in infected roots. Certain soil bacteria, collectively called rhizobia, form a symbiotic interaction with legumes, leading to the formation of nitrogen-fixing root nodules. Sedentary endoparasitic nematodes, on the other hand, induce highly specialized feeding sites in infected plant roots from which they withdraw nutrients. In order to establish these new root structures, it is thought that these organisms use and manipulate the endogenous molecular and physiological pathways of their hosts. Over the years, evidence has accumulated reliably demonstrating the involvement of the plant hormone auxin. Moreover, the auxin responses during microbe-induced de novo organ formation seem to be dynamic, suggesting that plant-associated microbes can actively modify their host''s auxin transport. In this review, we focus on recent findings in auxin transport mechanisms during plant development and on how plant symbionts and parasites have evolved to manipulate these mechanisms for their own purposes.     

Spatial genetic structuring of baobab (Adansonia digitata, Malvaceae) in the traditional agroforestry systems of West Africa

This study evaluates the spatial genetic structure of baobab (Adansonia digitata) populations from West African agroforestry systems at different geographical scales using AFLP fingerprints. Eleven populations from four countries (Benin, Ghana, Burkina Faso, and Senegal) had comparable levels of genetic diversity, although the two populations in the extreme west (Senegal) had less diversity. Pairwise F(ST) ranged from 0.02 to 0.28 and increased with geographic distance, even at a regional scale. Gene pools detected by Bayesian clustering seem to be a byproduct of the isolation-by-distance pattern rather than representing actual discrete entities. The organization of genetic diversity appears to result essentially from spatially restricted gene flow, with some influences of human seed exchange. Despite the potential for relatively long-distance pollen and seed dispersal by bats within populations, statistically significant spatial genetic structuring within populations (SGS) was detected and gave a mean indirect estimate of neighborhood size of ca. 45. This study demonstrated that relatively high levels of genetic structuring are present in baobab at both large and within-population level, which was unexpected in regard to its dispersal by bats and the influence of human exchange of seeds. Implications of these results for the conservation of baobab populations are discussed.     

Gene Time E{chi}pression Warper: a tool for alignment, template matching and visualization of gene expression time series

An application tool for alignment, template matching and visualization of gene expression time series is presented. The core algorithm is based on dynamic time warping techniques used in the speech recognition field. These techniques allow for non-linear (elastic) alignment of temporal sequences of feature vectors and consequently enable detection of similar shapes with different phases. AVAILABILITY: The Java program, examples and a tutorial are available at http://www.psb.ugent.be/cbd/papers/gentxwarper/     

Conditions for stable parapatric coexistence between Boophilusdecoloratus and B. microplus ticks: a simulation study using the competitive Lotka-Volterra model

The autochthonous tick Boophilus decoloratus, and the invasive species Bo. microplus, the tick most threatening the livestock industry in Africa, show complex interactions in their interspecific rivalry. This study was conducted to specify the conditions under which the two competitors can co-exist in equilibrium, and to provide insight into their climate-dependant parapatric distribution in Tanzania. A model of the Lotka-Volterra type was used, taking into account population dispersal and interactions of various kinds. If the model allowed for immunity-mediated competition on cattle, reproductive interference, and an external mortality factor, it explained fairly well the field observation that the borderline between these ticks loosely follows the 22–23°C isotherm and the 58 mm isohyet (i.e. ~700 mm of annual rainfall total). Simulations fully compatible with the pattern of real co-existing populations of Bo. decoloratus and Bo. microplus, characterized by a pronounced population density trough and mutual exclusion of the two ticks on cattle in an intermediary zone between their distributional ranges, were, however, achieved only if the model also implemented a hypothetical factor responsible for some mortality upon encounter of one tick with the other, interpretable as an interaction through a shared pathogen(s). This study also demonstrated the importance of non-cattle hosts, enabling the autochthon to avoid competition with Bo. microplus, for the behaviour of the modelled system. The simulations indicate that a substantial reduction of wildlife habitats and consequently of Bo. decoloratus refugia, may accelerate the replacement of Bo. decoloratus with Bo. microplus much faster than climatic changes might do.     

Shifts in the distributional ranges of <Emphasis Type="Italic">Boophilus</Emphasis> ticks in Tanzania: evidence that a parapatric boundary between <Emphasis Type="Italic">Boophilus microplus</Emphasis> and <Emphasis Type="Italic">B. decoloratus</Emphasis> follows climate gradients

Based on a national tick survey conducted in Tanzania between 1998 and 2001, predictive maps of tick distribution for B. microplus and B. decoloratus were computed and compared with historical maps that originated about 40 years ago. The new data collected showed that except for extremely cold and dry areas B. microplus has extended its distribution range and is now present in all the northern regions of Tanzania, and that high suitability is currently recorded for most of the previously non-occupied areas. In contrast, B. decoloratus, once abundant in Tanzania, has largely retreated to highlands in north and central Tanzania and several other high-altitude refuges. Geostatistical analysis revealed a dissimilar character of distribution for the two species at a local and regional scale, as well as an antagonistic relationship between them in a spatial context. The Tanzania data suggest that an equilibrium phase with a stable parapatric boundary that follows a climate gradient has been achieved. The zone of overlap in the distribution ranges of B. microplus and B. decoloratus is characterized by a decreased infestation rate as well as mutual exclusion on infested cattle. This finding matches studies on parapatry with hybrid zones, where the latter zones that separate species tend to rest in density troughs. Analysis of the Tanzania data shows that the critical factor for the advance of B. microplus and the retreat of B. decoloratus is associated with the 58 mm isohyet and the 22–23°C isotherm and indicates a well developed higher-temperature tolerance for B. microplus. It can be anticipated that climate changes may enhance the spread of B. microplus and consequently Babesia bovis into new areas of the African continent.