Cancer evolution: Darwin and beyond

Clinical and laboratory studies over recent decades have established branched evolution as a feature of cancer. However, while grounded in somatic selection, several lines of evidence suggest a Darwinian model alone is insufficient to fully explain cancer evolution. First, the role of macroevolutionary events in tumour initiation and progression contradicts Darwin's central thesis of gradualism. Whole-genome doubling, chromosomal chromoplexy and chromothripsis represent examples of single catastrophic events which can drive tumour evolution. Second, neutral evolution can play a role in some tumours, indicating that selection is not always driving evolution. Third, increasing appreciation of the role of the ageing soma has led to recent generalised theories of age-dependent carcinogenesis. Here, we review these concepts and others, which collectively argue for a model of cancer evolution which extends beyond Darwin. We also highlight clinical opportunities which can be grasped through targeting cancer vulnerabilities arising from non-Darwinian patterns of evolution

On the enumeration of finite LL-algebras

We use Constraint Satisfaction Methods to construct and enumerate finite $L$-algebras up to isomorphism. These objects were recently introduced by Rump and appear in Garside theory, algebraic logic, and the study of the combinatorial Yang-Baxter equation. There are 377322225 isomorphism classes of $L$-algebras of size eight. The database constructed suggest the existence of bijections between certain classes of $L$-algebras and well-known combinatorial objects. On the one hand, we prove that Bell numbers enumerate isomorphism classes of finite linear $L$-algebras. On the other hand, we also prove that finite regular $L$-algebras are in bijective correspondence with infinite-dimensional Young diagrams.Comment: 17 pages, 3 tables, 2 figures. Postprint versio

O impacto do homem na estrutura de uma espécie: Portugal, um paradigma

A bacia do Mediterrâneo é caracterizada pelo tradicional desaparecimento da floresta devido à acção do Homem e o impacto humano tem tido influência na alteração da diversidade genética. O pinheiro bravo ocorre em populações fragmentadas na região oeste da bacia do Mediterrâneo e a sua área de distribuição tem sido alterada nos últimos séculos devido a intensa florestação, em particular no SW de França e no Noroeste da Península Ibérica e, também, devido ao comportamento invasivo desta espécie em áreas perturbadas do ponto de vista ecológico. Nesta apresentação pretendemos sintetizar e discutir o resultado de estudos que utilizaram técnicas moleculares para revelar a diversidade do pinheiro bravo e, também, o impacto humano na sua estrutura genética; que é demonstrado paradigmaticamente em Portugal. Os parâmetros genéticos estimados com base em microsatélites do cloroplasto (cpSSR) revelaram que a diversidade genética é muito elevada ao nível da distribuição da espécie. Observou-se uma clara e significativa diferenciação entre grupos de populações de diferente origem geográfica (Portugal, França, Itália, Espanha e Marrocos). Pelo contrário, o grau de divergência dentro dos países é geralmente muito baixo ou próximo de zero, o que indica uma variação homogénea dentro dos grupos. A presença de diferenciação entre grupos de populações de diferentes áreas reflecte a existência de diferentes refúgios durante o Quaternário. Em França, o padrão haplotípico sugere uma mistura de material proveniente de diferentes origens. Só foram encontrados 3 mitótipos, usando marcadores mitocondriais, marcador de herança maternal, o que proporciona uma imagem clara de áreas colonizadas a partir dos diferentes refúgios; nem uma só população possui uma composição mista. Uma análise filogenética feita com base em isoenzimas mostrou que a estrutura geográfica do pinheiro bravo na Península Ibérica (PI) é muito elevada. As populações de Noroeste formam um grupo e as de Sudeste outro. Observou-se níveis elevados de diversidade nas populações de Este e Sul e uma redução importante da variabilidade em populações da região Noroeste da PI. No entanto, pode ter existido em Portugal um refúgio, pois o pinheiro bravo pode ter sobrevivido durante a última glaciação em zonas abrigadas e de baixa altitude junto ao Oceano Atlântico, o que parece também ser evidente devido a descobertas de pólen e carvão fóssil. A distribuição da variação genética do pinheiro bravo em Portugal, observada através de cpSSR indica que a diferenciação entre populações é baixa e que a diversidade existe principalmente dentro das populações. Não se observa nenhum padrão geográfico, mas as evidências existentes de uma forte influência antrópica antropogénica associada a um fluxo genético extensivo poderiam explicar esse resultado

Shrinking Weibel‐Palade bodies prevents high platelet recruitment in assays using thrombotic thrombocytopenic purpura plasma

Background: Thrombotic thrombocytopenic purpura (TTP), caused by a genetic or autoimmune-driven lack of ADAMTS-13 activity, leads to high levels of the ultra-large von Willebrand factor (VWF) multimers produced by endothelial cells, causing excess platelet recruitment into forming thrombi, often with mortal consequences. Treatments include plasma infusion or replacement to restore ADAMTS-13 activity, or prevention of platelet recruitment to VWF. // Objectives: We tested a different approach, exploiting the unique cell biology of the endothelium. Upon activation, the VWF released by exocytosis of Weibel-Palade bodies (WPBs), transiently anchored to the cell surface, unfurls as strings into flowing plasma, recruiting platelets. Using plasma from patients with TTP increases platelet recruitment to the surface of cultured endothelial cells under flow. WPBs are uniquely plastic, and shortening WPBs dramatically reduces VWF string lengths and the recruitment of platelets. We wished to test whether the TTP plasma-driven increase in platelet recruitment would be countered by reducing formation of the longest WPBs that release longer strings. // Methods: Endothelial cells grown in flow chambers were treated with fluvastatin, one of 37 drugs shown to shorten WPBs, then activated under flow in the presence of platelets and plasma of either controls or patients with TTP. // Result: We found that the dramatic increase in platelet recruitment caused by TTP plasma is entirely countered by treatment with fluvastatin, shortening the WPBs. // Conclusions: This potential approach of ameliorating the endothelial contribution to thrombotic risk by intervening far upstream of hemostasis might prove a useful adjunct to more conventional and direct therapies

von Willebrand factor/ADAMTS13 ratio at presentation of acute ischemic brain injury is predictive of outcome

Acute ischemic stroke (IS) and transient ischemic attack (TIA) are associated with raised von Willebrand factor (VWF) and decreased ADAMTS13 activity (ADAMTS13Ac). Their impact on mortality and morbidity is unclear. We conducted a prospective investigation of the VWF-ADAMTS13 axis in 292 adults (acute IS, n = 103; TIA, n = 80; controls, n = 109) serially from presentation until >6 weeks. The National Institutes of Health Stroke Score (NIHSS) and modified Rankin scale (mRS) were used to assess stroke severity. Presenting median VWF antigen (VWF:Ag)/ADAMTS13Ac ratios were: IS, 2.42 (range, 0.78-9.53); TIA, 1.89 (range, 0.41-8.14); and controls, 1.69 (range, 0.25-15.63). Longitudinally, the median VWF:Ag/ADAMTS13Ac ratio decreased (IS, 2.42 to 1.66; P = .0008; TIA, 1.89 to 0.65; P 2.6 predicted mortality (odds ratio, 6.33; range, 2.22-18.1). Those with a VWF:Ag/ADAMTS13Ac ratio in the highest quartile (>3.091) had 31% increased risk mortality. VWF:Ag/ADAMTS13Ac ratio at presentation of ischemic brain injury was associated with higher mRS (P = .021) and NIHSS scores (P = .029) at follow-up. Thrombolysis resulted in prompt reduction of the VWF:Ag/ADAMTS13Ac ratio and significant improvement in mRS on follow-up. A raised VWF:Ag/ADAMTS13Ac ratio at presentation of acute IS or TIA is associated with increased mortality and poorer functional outcome. A ratio of 2.6 seems to differentiate outcome. Prompt reduction in the ratio in thrombolysed patients was associated with decreased mortality and morbidity. The VWF:Ag/ADAMTS13Ac ratio is a biomarker for the acute impact of an ischemic event and longer-term outcome

Molecular evidence for the natural production of homozygous Cupressus sempervirens L. lines by Cupressus dupreziana seed trees

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Pharmacokinetics of plasma infusion in congenital thrombotic thrombocytopenic purpura.

BACKGROUND: Congenital thrombotic thrombocytopenic purpura (TTP) is defined by persistent severe deficiency of ADAMTS-13 in the absence of anti-ADAMTS-13 inhibitory antibodies, confirmed by mutational analysis. Replacement of the missing protease prevents disease relapse, primarily using plasma infusion (PI). OBJECTIVES, PATIENTS AND METHODS: There is scant evidence regarding optimal dose and frequency of treatment, tending to be empirically guided. We present a pharmacokinetic analysis of ADAMTS-13 in 6 patients with congenital TTP on established regimes following PI. RESULTS: We found a median clearance of 25.41ml/h and half-life of 130 hours, ranging between 82.6 and 189.5 hours (3.4 to 7.9 days respectively). All patients reached baseline ADAMTS-13 level within 7-10 days post plasma. Median ADAMTS-13 activity peak post PI was 24.05IU/dL. Variation was related to elimination rate, in turn affected by weight and metabolism, but not to von Willebrand factor antigen or activity levels. Using the pharmacokinetic parameters, we simulated individualised protocols based on PI dose or frequency to target hypothetical optimal plasma levels of ADAMTS-13 of 10 and 50IU/dL respectively. Results suggest a target trough ADAMTS-13 of 10IU/dL is feasible but 50IU/dL would not be achievable taking into account volume required. CONCLUSIONS: Further work is needed to compare treatment of congenital TTP with PI versus recombinant ADAMTS-13. PI may provide longer duration of ADAMTS-13 effect, but is limited by plasma volume required, whereas recombinant therapy can provide a higher ADAMTS-13 peak. We propose that investigation of interindividual clearance of ADAMTS-13 is necessary to optimise treatment, to enable rationale for dose and frequency of prophylaxis

Causes and consequences of large clonal assemblies in a poplar hybrid zone.

Asexual reproduction is a common and fundamental mode of reproduction in plants. Although persistence in adverse conditions underlies most known cases of clonal dominance, proximal genetic drivers remain unclear, in particular for populations dominated by a few large clones. In this paper, we studied a clonal population of the riparian tree Populus alba in the Douro river basin (northwestern Iberian Peninsula) where it hybridizes with P. tremula, a species that grows in highly contrasted ecological conditions. We used 73 nuclear microsatellites to test whether genomic background (species ancestry) is a relevant cause of clonal success, and to assess the evolutionary consequences of clonal dominance by a few genets. Additional Genotyping-by-Sequencing (GBS) data were produced to estimate the age of the largest clones. We found that a few ancient (over a few thousand years old) and widespread genets dominate the population, both in terms of clone size and number of sexual offspring produced. Interestingly, large clones possessed two genomic regions introgressed from P. tremula, which may have favored their spread under stressful environmental conditions. At the population level, the spread of large genets was accompanied by an overall ancient (>0.1 Myr) but soft decline of effective population size. Despite this decrease, and the high clonality and dominance of sexual reproduction by large clones, the Douro hybrid zone still displays considerable genetic diversity and low inbreeding. This suggests that, even in extreme cases as in the Douro, asexual and sexual dominance of a few large, geographically-extended individuals does not threaten population survival. This article is protected by copyright. All rights reserved

The role of forest genetic resources in responding to biotic and abiotic factors in the context of anthropogenic climate change

The current distribution of forest genetic resources on Earth is the result of a combination of natural processes and human actions. Over time, tree populations have become adapted to their habitats including the local ecological disturbances they face. As the planet enters a phase of human-induced climate change of unprecedented speed and magnitude, however, previously locally-adapted populations are rendered less suitable for new conditions, and ‘natural’ biotic and abiotic disturbances are taken outside their historic distribution, frequency and intensity ranges. Tree populations rely on phenotypic plasticity to survive in extant locations, on genetic adaptation to modify their local phenotypic optimum or on migration to new suitable environmental conditions. The rate of required change, however, may outpace the ability to respond, and tree species and populations may become locally extinct after specific, but as yet unknown and unquantified, tipping points are reached. Here, we review the importance of forest genetic resources as a source of evolutionary potential for adaptation to changes in climate and other ecological factors. We particularly consider climate-related responses in the context of linkages to disturbances such as pests, diseases and fire, and associated feedback loops. The importance of management strategies to conserve evolutionary potential is emphasised and recommendations for policy-makers are provided