Selection and inertia in the evolution of holocentric chromosomes in sedges (Carex, Cyperaceae)

? Changes in chromosome number as a result of fission and fusion in holocentrics have direct and immediate effects on the recombination rate. We investigate the support for the classic hypothesis that environmental stability selects for increased recombination rates. ? We employed a phylogenetic and cytogenetic data set from one of the most diverse angiosperm genera in the world, which has the largest nonpolyploid chromosome radiation (Carex, Cyperaceae; 2n = 12-124; 2100 spp.). We evaluated alternative Ornstein-Uhlenbeck models of chromosome number adaptation to the environment in an information-theoretic framework. ? We found moderate support for a positive influence of lateral inflorescence unit size on chromosome number, which may be selected in a stable environment in which resources for reproductive investment are larger. We found weak support for a positive influence on chromosome number of water-saturated soils and among-month temperature constancy, which would be expected to be negatively select for pioneering species. Chromosome number showed a strong phylogenetic signal. ? We argue that our finding of small but significant effects of life history and ecology is compatible with our original hypothesis regarding selection of optima in recombination rates: low recombination rate is optimal when inmediate fitness is required. By contrast, high recombination rate is optimal when stable environments allow for evolutionary innovation.     

Standardization efforts of digital pathology in Europe

BACKGROUND: EURO-TELEPATH is a European COST Action IC0604. It started in 2007 and will end in November 2011. Its main objectives are evaluating and validating the common technological framework and communication standards required to access, transmit, and manage digital medical records by pathologists and other medical specialties in a networked environment. BUSINESS MODELLING: Working Group 1, "Business Modelling in Pathology," has designed main pathology processes - Frozen Study, Formalin Fixed Specimen Study, Telepathology, Cytology, and Autopsy - using Business Process Modelling Notation (BPMN). INFORMATICS STANDARDS IN PATHOLOGY: Working Group 2 has been dedicated to promoting the application of informatics standards in pathology, collaborating with Integrating Healthcare Enterprise (IHE), Digital Imaging and Communications in Medicine (DICOM), Health Level Seven (HL7), and other standardization bodies. CONCLUSIONS: Health terminology standardization research has become a topic of great interest. Future research work should focus on standardizing automatic image analysis and tissue microarrays imaging.     

Diversification rates and chromosome evolution in the most diverse angiosperm genus of the temperate zone (Carex, Cyperaceae)

The sedge family (Cyperaceae: Poales; ca. 5600 spp.) is a hyperdiverse cosmopolitan group with centres of species diversity in Africa, Australia, eastern Asia, North America, and the Neotropics. Carex, with ca. 40% of the species in the family, is one of the most species-rich angiosperm genera and the most diverse in temperate regions of the Northern Hemisphere, making it atypical among plants in that it inverts the latitudinal gradient of species richness. Moreover, Carex exhibits high rates of chromosome rearrangement via fission, fusion, and translocation, which distinguishes it from the rest of the Cyperaceae. Here, we use a phylogenetic framework to examine how the onset of contemporary temperate climates and the processes of chromosome evolution have influenced the diversification dynamics of Carex. We provide estimates of diversification rates and map chromosome transitions across the evolutionary history of the main four clades of Carex. We demonstrate that Carex underwent a shift in diversification rates sometime between the Late Eocene and the Oligocene, during a global cooling period, which fits with a transition in diploid chromosome number. We suggest that adaptive radiation to novel temperate climates, aided by a shift in the mode of chromosome evolution, may explain the large-scale radiation of Carex and its latitudinal pattern of species richness.     

Exploring the diversity of bacterial communities in sediments of urban mangrove forests

Municipal sewage, urban runoff and accidental oil spills are common sources of pollutants in urban mangrove forests and may have drastic effects on the microbial communities inhabiting the sediment. However, studies on microbial communities in the sediment of urban mangroves are largely lacking. In this study, we explored the diversity of bacterial communities in the sediment of three urban mangroves located in Guanabara Bay (Rio de Janeiro, Brazil). Analysis of sediment samples by means of denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments suggested that the overall bacterial diversity was not significantly affected by the different levels of hydrocarbon pollution at each sampling site. However, DGGE and sequence analyses provided evidences that each mangrove sediment displayed a specific structure bacterial community. Although primer sets for Pseudomonas, alphaproteobacterial and actinobacterial groups also amplified ribotypes belonging to taxa not intended to be enriched, sequence analyses of dominant DGGE bands revealed ribotypes related to Alteromonadales, Burkholderiales, Pseudomonadales, Rhodobacterales and Rhodocyclales. Members of these groups were often shown to be involved in aerobic or anaerobic degradation of hydrocarbon pollutants. Many of these sequences were only detected in the sampling sites with high levels of anthropogenic inputs of hydrocarbons. Many dominant DGGE ribotypes showed low levels of sequence identity to known sequences, indicating a large untapped bacterial diversity in mangrove ecosystems.     

Systematics and evolution of Carex sects. Spirostachyae and Elatae (Cyperaceae)

Carex sect. Spirostachyae comprises 25 species displaying the centre of diversity in Eurasia, while sect. Elatae comprises 22 species displaying the centre of diversity in tropical African mountainous regions. Phylogenetic analysis of the 136 ITS and 108 5′trnK intron sequences of 23 species of sect. Spirostachyae and 20 species of sect. Elatae revealed that neither section is monophyletic. With the exclusion of C. montis-eeka (sect. Spirostachyae) and C. insularis, C. iynx and C. longibrachiata (sect. Elatae), the sects. Spirostachyae and Elatae constitute a monophyletic group of 38 species, 22 of which were previously included in sect. Spirostachyae and 16 of which were in sect. Elatae (considering C. thomasii as C. mannii ssp. thomasii). Two main groups with different edaphic preferences were identified in the core Spirostachyae, in congruence with some morphological features. One group comprises primarily acidophilus species including 11 species of sect. Spirostachyae and 16 species of sect. Elatae. The other group includes 11 basophilic species of sect. Spirostachyae. Incongruence between nuclear and plastid genomes was detected, suggesting hybridization or lineage sorting processes in the evolution of the core Spirostachyae.     

Digital pathology in personalized cancer therapy

The development of small molecule inhibitors of growth factor receptors, and the discovery of somatic mutations of the tyrosine kinase domain, have resulted in new paradigms for cancer therapy. Digital microscopy is an important tool for surgical pathologists. The achievements in the digital pathology field have modified the workflow of pathomorphology labs, enhanced the pathologist's role in diagnostics, and increased their contribution to personalized targeted medicine. Digital image analysis is now available in a variety of platforms to improve quantification performance of diagnostic pathology. We here describe the state of digital microscopy as it applies to the field of quantitative immunohistochemistry of biomarkers related to the clinical personalized targeted therapy of breast cancer, non-small lung cancer and colorectal cancer: HER-2, EGFR, KRAS and BRAF genes. The information is derived from the experience of the authors and a review of the literature.