Visual cavity analysis in molecular simulations

Molecular surfaces provide a useful mean for analyzing interactions between biomolecules; such as identification and characterization of ligand binding sites to a host macromolecule. We present a novel technique, which extracts potential binding sites, represented by cavities, and characterize them by 3D graphs and by amino acids. The binding sites are extracted using an implicit function sampling and graph algorithms. We propose an advanced cavity exploration technique based on the graph parameters and associated amino acids. Additionally, we interactively visualize the graphs in the context of the molecular surface. We apply our method to the analysis of MD simulations of Proteinase 3, where we verify the previously described cavities and suggest a new potential cavity to be studied

Oligo-DNA Custom Macroarray for Monitoring Major Pathogenic and Non-Pathogenic Fungi and Bacteria in the Phyllosphere of Apple Trees

BACKGROUND: To monitor the richness in microbial inhabitants in the phyllosphere of apple trees cultivated under various cultural and environmental conditions, we developed an oligo-DNA macroarray for major pathogenic and non-pathogenic fungi and bacteria inhabiting the phyllosphere of apple trees. METHODS AND FINDINGS: First, we isolated culturable fungi and bacteria from apple orchards by an agar-plate culture method, and detected 32 fungal and 34 bacterial species. Alternaria, Aureobasidium, Cladosporium, Rhodotorula, Cystofilobasidium, and Epicoccum genera were predominant among the fungi, and Bacillus, Pseudomonas, Sphingomonas, Methylobacterium, and Pantoea genera were predominant among the bacteria. Based on the data, we selected 29 major non-pathogenic and 12 phytopathogenic fungi and bacteria as the targets of macroarray. Forty-one species-specific 40-base pair long oligo-DNA sequences were selected from the nucleotide sequences of rDNA-internal transcribed spacer region for fungi and 16S rDNA for bacteria. The oligo-DNAs were fixed on nylon membrane and hybridized with digoxigenin-labeled cRNA probes prepared for each species. All arrays except those for Alternaria, Bacillus, and their related species, were specifically hybridized. The array was sensitive enough to detect 10(3) CFU for Aureobasidium pullulans and Bacillus cereus. Nucleotide sequencing of 100 each of independent fungal rDNA-ITS and bacterial 16S-rDNA sequences from apple tree was in agreement with the macroarray data obtained using the same sample. Finally, we analyzed the richness in the microbial inhabitants in the samples collected from apple trees in four orchards. Major apple pathogens that cause scab, Alternaria blotch, and Marssonina blotch were detected along with several non-phytopathogenic fungal and bacterial inhabitants. CONCLUSIONS: The macroarray technique presented here is a strong tool to monitor the major microbial species and the community structures in the phyllosphere of apple trees and identify key species antagonistic, supportive or co-operative to specific pathogens in the orchard managed under different environmental conditions

Virtual unfolding of folded papyri

The historical importance of ancient manuscripts is unique since they provide information about the heritage of ancient cultures. Often texts are hidden in rolled or folded documents. Due to recent improvements in sensitivity and resolution, spectacular disclosures of rolled hidden texts were possible by X-ray tomography. However, revealing text on folded manuscripts is even more challenging. Manual unfolding is often too risky in view of the fragile condition of fragments, as it can lead to the total loss of the document. X-ray tomography allows for virtual unfolding and enables non-destructive access to hidden texts. We have recently demonstrated the procedure and tested unfolding algorithms on a mockup sample. Here, we present results on unfolding ancient papyrus packages from the papyrus collection of the Musée du Louvre, among them objects folded along approximately orthogonal folding lines. In one of the packages, the first identification of a word was achieved, the Coptic word for “Lord”

Molerområdets geologi – sedimenter, fossiler, askelag og glaicaltektonik

Abstract in Danish I den vestlige del af Limfjorden findes en række kystklinter, hvor eocæne lag er blottet. Moler er en ca. 55-56 millioner år gammel diatomit, som indeholder lag af uforvitret vulkansk aske samt et stort antal velbevarede marine og terrestriske fossiler. Stolleklint Leret og Fur Formationen har et usædvanligt fossilselskab med mange repræsentanter for insekter, fisk, fugle og skildpadder men meget få kalkskallede, hvirvelløse dyr. De vulkanske askelag afspejler et stort antal gigantiske, eksplosive udbrud inden for en kort periode, hvor lavatilstrømningen var stor, samtidig med at udbruddene skete på lavt vand i den nydannede oceanbund. For ca. 25.000 år siden dannede fremrykkende iskapper folder og overskydninger i moler, askelag og glaciale sedimenter. Molerområdets geologi kan sammenfattes i følgende citat: ”…talrige tynde lag af sort vulkansk Aske...træde selv på lang Afstand tydelig frem i det hvide Moler …[Da de] ofte danner store Bugter og Folder, vil man forstaa, at de høje lyse Molerklinter i Solskin frembyde et malerisk og ejendommeligt Skue.” (N. V. Ussing i ’Danmarks Geologi’ 1904, s.143)

Microbiology of the phyllosphere: a playground for testing ecological concepts

Many concepts and theories in ecology are highly debated, because it is often difficult to design decisive tests with sufficient replicates. Examples include biodiversity theories, succession concepts, invasion theories, coexistence theories, and concepts of life history strategies. Microbiological tests of ecological concepts are rapidly accumulating, but have yet to tap into their full potential to complement traditional macroecological theories. Taking the example of microbial communities on leaf surfaces (i.e. the phyllosphere), we show that most explorations of ecological concepts in this field of microbiology focus on autecology and population ecology, while community ecology remains understudied. Notable exceptions are first tests of the island biogeography theory and of biodiversity theories. Here, the phyllosphere provides the unique opportunity to set up replicated experiments, potentially moving fields such as biogeography, macroecology, and landscape ecology beyond theoretical and observational evidence. Future approaches should take advantage of the great range of spatial scales offered by the leaf surface by iteratively linking laboratory experiments with spatial simulation models

Multitasking, but for what benefit? The dilemma facing Nigerian university students regarding part-time working.

Students working part-time while studying for a full-time university degree are commonplace in many Western countries. This paper however, examines the historically uncommon part-time working activities and career aspirations among Nigerian university students. In particular, how working is perceived to contribute to developing employability skills, and whether it is influenced by their self-efficacy. Survey data from 324 questionnaires was collected from a federal university, although the data analysis used a mixed-method. The findings indicate that despite low levels of part-time working generally among students, older, more experienced, higher level and female students, place a premium on the skills that part-time work can develop. Moreover, self-efficacy and being female, is a significant predictor in understanding part-time work and career aspirations. This study offers originality by focusing on students’ part-time work, the value working provides, and its link with career aspirations, within a relatively unexplored context of Nigeria