Self-destructive percolation, invasion percolation and related models

Meester, R.W.J. [Promotor]Berg, J. van den [Promotor

Continuity for self-destructive percolation in the plane

A few years ago two of us introduced, motivated by the study of certain forest-fireprocesses, the self-destructive percolation model (abbreviated as sdp model). A typical configuration for the sdp model with parameters p and delta is generated in three steps: First we generate a typical configuration for the ordinary percolation model with parameter p. Next, we make all sites in the infinite occupied cluster vacant. Finally, each site that was already vacant in the beginning or made vacant by the above action, becomes occupied with probability delta (independent of the other sites). Let theta(p, delta) be the probability that some specified vertex belongs, in the final configuration, to an infinite occupied cluster. In our earlier paper we stated the conjecture that, for the square lattice and other planar lattices, the function theta has a discontinuity at points of the form (p_c, delta), with delta sufficiently small. We also showed remarkable consequences for the forest-fire models. The conjecture naturally raises the question whether the function theta is continuous outside some region of the above mentioned form. We prove that this is indeed the case. An important ingredient in our proof is a (somewhat stronger form of a) recent ingenious RSW-like percolation result of Bollob\'{a}s and Riordan

Candida parapsilosis secreted lipase as an important virulence factor

The prevalence of Candida parapsilosis, an opportunistic human pathogenic fungal species, is increasing at an alarming rate in the hospital environment. Patients at risk for C. parapsilosis infection include those with immunosuppression, such as individuals with cancer, AIDS, and low birth weight premature neonates as well as patients that had undergone abdominal surgery. Neonatal candidiasis caused by C. parapsilosis has been widely reported across the globe. Various reports have shown that, compared to other Candida species, certain C. parapsilosis clinical isolates were less susceptible to antifungals such as amphotericin B, fluconazole, and caspofungin. In addition, some studies have even reported multi-echinocandin or multi-azole resistant strains of C. parapsilosis. C. parapsilosis has several virulence factors that contribute to its capacity for host invasion and among these factors extracellular lipases have a major role in pathogenesis. In this review we have collected all the recent relevant studies that confirm the involvement of secreted lipases in C. parapsilosis pathogenesis, using both in vitro and in vivo models of infection. Of particular note, an available lipase deficient C. parapsilosis strain has been utilized to demonstrate that the lack of secreted lipases decreased virulence, reduced tissue damage, and was less able to survive within phagocytes or mice compared to the wild type. Since fungal secreted lipases have different characteristics than lipolytic enzymes present in humans, C. parapsilosis extracellular lipases may be potential targets for the development of novel antifungal drugs

Prehistoric anthropogenic introduction of partulid tree snails in Papua New Guinean archipelagos

Aim  Members of the tropical tree snail family Partulidae are endemic to Pacific high oceanic islands and typically have single‐island ranges. Two nominal Papua New Guinean species, Partula carteriensis and Partula similaris , deviate from familial norms by having extensive multi‐island ranges that include low islands. We hypothesized that undocumented anthropogenic introductions may underlie this regional biogeographical anomaly and evaluated this hypothesis with novel field distributional and genotypic data. Location  Papua New Guinean archipelagos between 1.4 and 11.4° S and 146.5 and 154.2° E. Methods  Ethanol‐preserved museum lots of P. carteriensis (from New Britain, Bismarck Archipelago) and P. similaris (from Woodlark, Boiaboiawaga and Goodenough islands) were genotyped for a standard mitochondrial marker, cytochrome c oxidase subunit I (COI), and the resulting haplotypes were subjected to phylogeographical analyses. Results  All four genotyped populations showed very little genetic or conchological differentiation, irrespective of nominal taxonomic status, the archipelago sampled or whether the island was low, high, oceanic or continental. Partula carteriensis and P. similaris exhibit atypical distributions on larger high islands, being restricted to coastal villages and absent from native forest. Main conclusions  Our results strongly indicate that P. carteriensis and P. similaris are conspecific, although a formal taxonomic revision is beyond the scope of this present study. They collectively exhibit the most heterogeneous geographical range known among partulids and their explicitly synanthropic association with high island coastal villages strongly implicates human introduction as the regional dispersal mechanism. We currently lack insights into the timeframe (apart from regional prehistory) and cultural context of these translocations. We also lack a convincing source population, and it may be necessary to survey the partulid fauna of the neighbouring Solomon Islands to identify one. Partulids are critically endangered throughout much of their range and the discovery of populations that apparently thrive in human‐altered landscapes is noteworthy. Their study may provide clues of broad relevance to partulid conservation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/86895/1/j.1365-2699.2011.02489.x.pd

Alpine Crossroads or Origin of Genetic Diversity? Comparative Phylogeography of Two Sympatric Microgastropod Species

The Alpine Region, constituting the Alps and the Dinaric Alps, has played a major role in the formation of current patterns of biodiversity either as a contact zone of postglacial expanding lineages or as the origin of genetic diversity. In our study, we tested these hypotheses for two widespread, sympatric microgastropod taxa – Carychium minimum O.F. Müller, 1774 and Carychium tridentatum (Risso, 1826) (Gastropoda, Eupulmonata, Carychiidae) – by using COI sequence data and species potential distribution models analyzed in a statistical phylogeographical framework. Additionally, we examined disjunct transatlantic populations of those taxa from the Azores and North America. In general, both Carychium taxa demonstrate a genetic structure composed of several differentiated haplotype lineages most likely resulting from allopatric diversification in isolated refugial areas during the Pleistocene glacial periods. However, the genetic structure of Carychium minimum is more pronounced, which can be attributed to ecological constraints relating to habitat proximity to permanent bodies of water. For most of the Carychium lineages, the broader Alpine Region was identified as the likely origin of genetic diversity. Several lineages are endemic to the broader Alpine Region whereas a single lineage per species underwent a postglacial expansion to (re)colonize previously unsuitable habitats, e.g. in Northern Europe. The source populations of those expanding lineages can be traced back to the Eastern and Western Alps. Consequently, we identify the Alpine Region as a significant ‘hot-spot’ for the formation of genetic diversity within European Carychium lineages. Passive dispersal via anthropogenic means best explains the presence of transatlantic European Carychium populations on the Azores and in North America. We conclude that passive (anthropogenic) transport could mislead the interpretation of observed phylogeographical patterns in general

Finding needles in haystacks : linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.The Intramural Research Programs of the National Center for Biotechnology Information, National Library of Medicine and the National Human Genome Research Institute, both at the National Institutes of Health.http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353am201