Comparative genomics of trypanosomatid parasitic protozoa

A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that-along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions-have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont.     

Unmasking the S-phase-promoting potential of cyclin B1

In higher eukaryotes, the S phase and M phase of the cell cycle are triggered by different cyclin-dependent kinases (CDKs). For example, in frog egg extracts, Cdk1-cyclin B catalyzes entry into mitosis but cannot trigger DNA replication. Two hypotheses can explain this observation: Either Cdk1-cyclin B fails to recognize the key substrates of its S-phase-promoting counterparts, or its activity is somehow regulated to prevent it from activating DNA synthesis. Here, we show that Cdk1-cyclin B1 has cryptic S-phase-promoting abilities that can be unmasked by relocating it from the cytoplasm to the nucleus and moderately stimulating its activity. Subcellular localization of vertebrate CDKs and the control of their activity are thus critical factors for determining their specificity.     

Gastric cancer originating from bone marrow-derived cells

Epithelial cancers are believed to originate from transformation of tissue stem cells. However, bone marrow-derived cells (BMDCs), which are frequently recruited to sites of tissue injury and inflammation, might also represent a potential source of malignancy. We show that although acute injury, acute inflammation, or transient parietal cell loss within the stomach do not lead to BMDC recruitment, chronic infection of C57BL/6 mice with Helicobacter, a known carcinogen, induces repopulation of the stomach with BMDCs. Subsequently, these cells progress through metaplasia and dysplasia to intraepithelial cancer. These findings suggest that epithelial cancers can originate from marrow-derived sources and thus have broad implications for the multistep model of cancer progression.     

Absence of geographical structure of morphological variation in <Emphasis Type="Italic">Juniperus oxycedrus</Emphasis> L. subsp. <Emphasis Type="Italic">oxycedrus</Emphasis> in the Balkan Peninsula

We examined leaf and mature seed cone variation of Juniperus oxycedrus L. subsp. oxycedrus in 12 natural populations across the species range in the Balkan Peninsula. We measured 10 morphological traits from a minimum of 100 leaves in each of 190 individuals, and two morphological traits from 30–50 seed cones in each of 94 females. High phenotypic variation was found, but no geographical structure or cline across populations was detected for any of the studied traits. Mean values of comparable leaf and cone morphological traits did not differ considerably from values reported elsewhere. Gender dimorphism in leaf morphology was detected, but it was not distributed uniformly throughout the studied area. An ANOVA model with both nested and crossed effects revealed that the largest proportion of the total variation was, as expected, contained within populations, partly as among-tree variation (18–47%, depending on the trait) and partly as within-tree variation (33–77%), which was remarkably high. Gender dimorphism explained only 0–3% of the total variation. Differences among populations (2–23%) were significant for all studied traits except one; however, PCA showed no clear geographical differentiation of the studied populations. This lack of phylogeographical structure may be the consequence of repeatedly occurring colonisation-retreat scenarios and suggests the existence of several small refugial populations scattered over a large part of the Balkan Peninsula in the Pleistocene. Further research including palaeobotanical and molecular genetic studies will be needed to better understand the forces that shaped current variation patterns of J. oxycedrus L. subsp. oxycedrus in the Balkan Peninsula.     

Pathogenic Botryosphaeriaceae associated with <Emphasis Type="Italic">Mangifera indica</Emphasis> in the Kimberley Region of Western Australia

Members of the Botryosphaeriaceae, in particular Lasiodiplodia theobromae, Neofusicoccum parvum, N. mangiferum and Botryosphaeria dothidea, commonly cause stem cankers, dieback and stem end rot of mangoes worldwide. In the current study, eight taxa of Botryosphaeriaceae were identified as canker-associated fungi, pathogens, potential pathogens or endophytes of mangoes in the Kimberley, Australia. These include Neoscytalidium novaehollandiae, Ne. dimidiatum, Pseudofusicoccum adansoniae, P. ardesiacum, P. kimberleyense, Lasiodiplodia sp. 1, L. iraniensis and L. pseudotheobromae. The pathogenicity of a selection of these species toward fruit and branches was tested. All were pathogenic to mango in comparison to the control, with Lasiodiplodia spp. being the most pathogenic. It appears that either geographic isolation or the unique growing conditions in the Kimberley may have provided an effective barrier to the acquisition or establishment of known botryosphaeriaceous pathogens. Wounds caused by mechanical pruning may provide an entry point for infection, whilst severe pruning may increase plant stress.     

Relative effects of management and environmental conditions on performance and survival of populations of a terrestrial orchid, Dactylorhiza majalis

For population viability analysis of endangered orchid populations, it is crucial to disentangle the effects of weather and management from intrinsic orchid dynamics. When doing this, typically several months’ average temperatures and/or sums of precipitations are compared with some characteristics of plant performance. Here we tested, whether short averaging intervals (1-2 weeks) are more closely correlated with orchid performance. We used 5 years of data from five Dactylorhiza majalis populations, and have shown that the improvement of prediction by shortening the interval over which the temperatures are averaged or precipitation summed, even if detectable, is only weak and not significant. This, however, may be due to low weather variability during the study. Regarding the second aspect, the effect of management (presence or absence of mowing), we have found that leaf area of D. majalis at the regularly mown site was larger than that at the sites which were mown only once in 2 years, but we did not detect a significant effect of the absence of mowing on the incidence of flowering. Mowing can affect orchid performance in two ways: by reduced shading of orchids and by reducing competition with other species. Therefore, we have determined the co-occurring species associated with presence or absence of mowing and found that shading significantly affected the length of the flower stalk, the ratio of leaf width to leaf length at the end of the season, but did not affect seed weight and probability of flowering the next year. We conclude that the most appropriate management for D. majalis is mowing at least once a year, ideally at the end of June/beginning of July, after its fruiting.     

Detecting interaction(s) and assessing the impact of component subsets in a chemical mixture using fixed-ratio mixture ray designs

An important environmental and regulatory issue is the protection of human health from potential adverse effects of cumulative exposure to multiple chemicals. Earlier literature suggested restricting inference to specific fixed-ratio rays of interest. Based on appropriate definitions of additivity, single chemical data are used to predict the relationship among the chemicals under the zero-interaction case. Parametric comparisons between the additivity model and the model fit along the fixed-ratio ray(s) are used to detect departure from additivity. Collection of data along reduced fixed-ratio rays, where subsets of chemicals of interest are removed from the mixture and the remaining compounds are at the same relative ratios as considered in the full ray, allow researchers to make inference about the effect of the removed chemicals. Methods for fitting simultaneous confidence bands about the difference between the best fitting model and the model predicted under additivity are developed to identify regions along the rays where significant interactions occur. This general approach is termed the “single chemicals required” (SCR) method of analysis. A second approach, termed “single chemicals not required” (SCNR) method of analysis, is based on underlying assumptions about the parameterization of the response surface. Under general assumptions, polynomial terms for models fit along fixed-ratio rays are associated with interaction terms. Consideration is given to the case where only data along the mixture rays are available. Tests of hypotheses, which consider interactions due to subsets of chemicals, are also developed.