Spatio-temporal Models of Lymphangiogenesis in Wound Healing

Several studies suggest that one possible cause of impaired wound healing is failed or insufficient lymphangiogenesis, that is the formation of new lymphatic capillaries. Although many mathematical models have been developed to describe the formation of blood capillaries (angiogenesis), very few have been proposed for the regeneration of the lymphatic network. Lymphangiogenesis is a markedly different process from angiogenesis, occurring at different times and in response to different chemical stimuli. Two main hypotheses have been proposed: 1) lymphatic capillaries sprout from existing interrupted ones at the edge of the wound in analogy to the blood angiogenesis case; 2) lymphatic endothelial cells first pool in the wound region following the lymph flow and then, once sufficiently populated, start to form a network. Here we present two PDE models describing lymphangiogenesis according to these two different hypotheses. Further, we include the effect of advection due to interstitial flow and lymph flow coming from open capillaries. The variables represent different cell densities and growth factor concentrations, and where possible the parameters are estimated from biological data. The models are then solved numerically and the results are compared with the available biological literature.Comment: 29 pages, 9 Figures, 6 Tables (39 figure files in total

Inferring Binding Energies from Selected Binding Sites

We employ a biophysical model that accounts for the non-linear relationship between binding energy and the statistics of selected binding sites. The model includes the chemical potential of the transcription factor, non-specific binding affinity of the protein for DNA, as well as sequence-specific parameters that may include non-independent contributions of bases to the interaction. We obtain maximum likelihood estimates for all of the parameters and compare the results to standard probabilistic methods of parameter estimation. On simulated data, where the true energy model is known and samples are generated with a variety of parameter values, we show that our method returns much more accurate estimates of the true parameters and much better predictions of the selected binding site distributions. We also introduce a new high-throughput SELEX (HT-SELEX) procedure to determine the binding specificity of a transcription factor in which the initial randomized library and the selected sites are sequenced with next generation methods that return hundreds of thousands of sites. We show that after a single round of selection our method can estimate binding parameters that give very good fits to the selected site distributions, much better than standard motif identification algorithms

A reexamination of information theory-based methods for DNA-binding site identification

<p>Abstract</p> <p>Background</p> <p>Searching for transcription factor binding sites in genome sequences is still an open problem in bioinformatics. Despite substantial progress, search methods based on information theory remain a standard in the field, even though the full validity of their underlying assumptions has only been tested in artificial settings. Here we use newly available data on transcription factors from different bacterial genomes to make a more thorough assessment of information theory-based search methods.</p> <p>Results</p> <p>Our results reveal that conventional benchmarking against artificial sequence data leads frequently to overestimation of search efficiency. In addition, we find that sequence information by itself is often inadequate and therefore must be complemented by other cues, such as curvature, in real genomes. Furthermore, results on skewed genomes show that methods integrating skew information, such as <it>Relative Entropy</it>, are not effective because their assumptions may not hold in real genomes. The evidence suggests that binding sites tend to evolve towards genomic skew, rather than against it, and to maintain their information content through increased conservation. Based on these results, we identify several misconceptions on information theory as applied to binding sites, such as negative entropy, and we propose a revised paradigm to explain the observed results.</p> <p>Conclusion</p> <p>We conclude that, among information theory-based methods, the most unassuming search methods perform, on average, better than any other alternatives, since heuristic corrections to these methods are prone to fail when working on real data. A reexamination of information content in binding sites reveals that information content is a compound measure of search and binding affinity requirements, a fact that has important repercussions for our understanding of binding site evolution.</p

Mitochondrial DNA and trade data support multiple origins of Helicoverpa armigera (Lepidoptera, Noctuidae) in Brazil

The Old World bollworm Helicoverpa armigera&nbsp;is now established in Brazil but efforts to identify incursion origin(s) and pathway(s) have met with limited success due to the patchiness of available data. Using international agricultural/horticultural commodity trade data and mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) and cytochrome b (Cyt b) gene markers, we inferred the origins and incursion pathways into Brazil. We detected 20 mtDNA haplotypes from six Brazilian states, eight of which were new to our 97 global COI-Cyt b&nbsp;haplotype database. Direct sequence matches indicated five Brazilian haplotypes had Asian, African, and European origins. We identified 45 parsimoniously informative sites and multiple substitutions per site within the concatenated (945 bp) nucleotide dataset, implying that probabilistic phylogenetic analysis methods are needed. High diversity and signatures of uniquely shared haplotypes with diverse localities combined with the trade data suggested multiple incursions and introduction origins in Brazil. Increasing agricultural/horticultural trade activities between the Old and New Worlds represents a significant biosecurity risk factor. Identifying pest origins will enable resistance profiling that reflects countries of origin to be included when developing a resistance management strategy, while identifying incursion pathways will improve biosecurity protocols and risk analysis at biosecurity hotspots including national ports

A arqueologia dos fermentados: a etílica história dos Tupi-Guarani

O consumo de bebidas fermentadas é geralmente negligenciado pela literatura arqueológica, que trata a questão como tema de interesse secundário (recreativo) na história das populações humanas. Entretanto, a literatura etnográfica das sociedades indígenas das terras baixas sul-americanas indica exatamente o oposto: é o alimento vegetal sólido e não alcoólico que tende a possuir um papel secundário na vida cotidiana e ritualística de diversos coletivos. Os dados arqueológicos aprofundam temporalmente essa relação entre o ser humano e os fermentados. Além disso, os vasos cerâmicos arqueológicos utilizados para o preparo e consumo desses fermentados são fundamentais para a compreensão de processos e eventos históricos que modelaram a dispersão de uma série de grupos pelo continente

A taxonomic backbone for the global synthesis of species diversity in the angiosperm order Caryophyllales

The Caryophyllales constitute a major lineage of flowering plants with approximately 12500 species in 39 families. A taxonomic backbone at the genus level is provided that reflects the current state of knowledge and accepts 749 genera for the order. A detailed review of the literature of the past two decades shows that enormous progress has been made in understanding overall phylogenetic relationships in Caryophyllales. The process of re-circumscribing families in order to be monophyletic appears to be largely complete and has led to the recognition of eight new families (Anacampserotaceae, Kewaceae, Limeaceae, Lophiocarpaceae, Macarthuriaceae, Microteaceae, Montiaceae and Talinaceae), while the phylogenetic evaluation of generic concepts is still well underway. As a result of this, the number of genera has increased by more than ten percent in comparison to the last complete treatments in the Families and genera of vascular plants” series. A checklist with all currently accepted genus names in Caryophyllales, as well as nomenclatural references, type names and synonymy is presented. Notes indicate how extensively the respective genera have been studied in a phylogenetic context. The most diverse families at the generic level are Cactaceae and Aizoaceae, but 28 families comprise only one to six genera. This synopsis represents a first step towards the aim of creating a global synthesis of the species diversity in the angiosperm order Caryophyllales integrating the work of numerous specialists around the world

Determinants of the Fynbos/Succulent Karoo biome boundary: Insights from a reciprocal transplant experiment

Boundaries between Fynbos and Succulent Karoo vegetation in the Greater Cape Floristic Region are frequently characterised by sharp transitions from sandy, dystrophic to loamy, mesotrophic soils, together with a more gradual climate transition from cooler, wetter conditions typical of Fynbos at higher elevations to warmer, drier conditions at lower elevations typical of Succulent Karoo. There is very high species turnover across these boundaries, providing an opportunity to disentangle the relative roles of climate and soil type in determining the biome boundary. A fully reciprocal transplant approach was employed here to investigate this question, using three species from each biome occurring naturally in close proximity at Jonaskop, Western Cape. Greenhouse-germinated and established seedlings of all species were planted into both sandy, dystrophic and loamy, mesotrophic soils typical of each biome at four sites along an elevational transect (elevations 545 m, 744 m, 953 m, 1303 m) at Jonaskop, and their growth and survivorship monitored for 7 months. At least one site on the elevation gradient represented annual climate rainfall and temperature conditions during the experimental period typical of the range edge for each of the selected species, this typically being the lowest elevation site (warm × dry) for Fynbos species (Protea humiflora, P. magnifica and P. amplexicaulis), and the highest elevation site (cool × wet) for Succulent Karoo species (Ruschia lineolata, Drosanthemum speciosum and Pteronia incana). Fynbos species showed significant adverse responses to loamy mesotrophic soil, with highly significant reductions in growth and high and rapid rates of mortality relative to their native soil. Fynbos species showed somewhat reduced growth and survival at the lowest elevation when grown in native soils, but demonstrated significant interaction between soil type and elevation with much lower growth and survival at the lowest elevation on the loamy soils. Surprisingly, all the Fynbos species showed reductions in growth and survival at the highest elevation, with significant reductions in two of the three species. Succulent Karoo species, by contrast, showed very few significant performance differences between soil types and few significant soil × elevation interactive effects, but did show significant growth and survival responses to elevation, with high growth and survival at mid-level elevations, far higher than their natural extent at the site. These results suggest that the selected Succulent Karoo species are neither edaphically nor climatically constrained from establishing and growing in sandy dystrophic soils and cool climates typical of the Fynbos vegetation along this elevation gradient, but that Fynbos species are strongly limited both edaphically and climatically from growing under conditions typical of the Succulent Karoo.We propose that Succulent Karoo elements may be excluded competitively or through disturbance from colonising sandy dystrophic soils at higher elevations in Fynbos vegetation, with fire regime most likely responsible for maintaining the sharply delineated boundaries between these biomes. This is because fire would strongly exclude non-fire adapted Succulent Karoo species at and above the biome boundary, while loamy soils and climate together would strongly exclude Fynbos species from the heavier soils of the Succulent Karoo. The relative climate and soil affinities of these biomes, accentuated by the role of fire, could therefore provide a coherent explanation for biome boundaries in the Greater Cape Floristic Region. We note however that the limited species selection in this study precludes a conclusive general result, and that several interesting questions remain about soil, climate and disturbance determinants across this biome boundary