PhyloDetect: a likelihood-based strategy for detecting microorganisms with diagnostic microarrays

MOTIVATION: Detection and identification of microbes using diagnostic arrays is still subject of ongoing research. Existing significance-based algorithms consider an organism detected even if a significant number of the microarray probes that match the organism are called absent in a hybridization. Further, they do generate redundant results if the target organisms show high sequence similarity and the microarray probes cannot discriminate all of them. RESULTS: We propose a new analysis strategy that considers organism similarities and calls organisms only present if the probes that match the organism but are absent in a hybridization can be explained by random events. In our strategy, we.rst identify the groups of target organisms that are actually distinguishable by the array. Subsequently, these organism groups are placed in a hierarchical tree such that groups matching only less specific probes are closer to the tree root, and groups that are discriminated only by few probes are close to each other. Finally, we compute for each group a likelihood score that is based on a hypothesis test with the null hypothesis that the group was actually present in the hybridized sample. We have validated our strategy using datasets from two different array types and implemented it as an easy-to-use web application. AVAILABILITY: http://www.fgcz.ethz.ch/PhyloDetect. SUPPLEMENTARY INFORMATION: Example data is available at http://www.fgcz.ethz.ch/PhyloDetect

On the diversity of Magdelainella Jeannel (Cholevidae, Coleoptera) in Serbia

Three new species of cholevid beetles, Magdelainella zivojindjordjevici n. sp. (southwestern Serbia), Magdelainella mucanjensis n. sp. (Mt. Mučanj Serbia), and Magdelainella nikolateslai n. sp. (Mt. Goč, Serbia) are described and diagnosed. All taxonomically important features (including female genitalia) are illustrated. Magdelainella noesskei (Apfelbeck) (from Bosnia and Herzegovina) is given full specific status and is clearly separated from M. serbica (Müller) (from Serbia). All new species are clearly distinct from other existing congeners. These forms are of Tertiary origin and age and represent both relicts and endemics inhabiting southwestern and central parts of Serbia, respectively

Spray ILGAR indium sulfide buffers for Cu In,Ga S,Se 2 solar cells

Thin film indium sulfide buffer layers have been prepared using the Spray ILGAR technique for use in chalcopyrite solar cells. Buffers deposited on commercially grown Cu In,Ga S,Se 2 absorbers have produced cells reaching a certified efficiency of 14.7 and average efficiencies matching the reference solar cells prepared with a conventional cadmium sulfide buffer layer. The process parameters have been optimized and the resulting cells have been studied using current voltage and temperature illumination dependent current voltage analysis as well as quantum efficiency measurement

Comparison of sampling and culture methods for the diagnosis of Tritrichomonas foetus infection in bulls

abstract: Sampling methods for preputial secretions and culture methods for T. foetus were compared in a 2-by-2 factorial experiment. 14 bulls were confirmed as infected by repeated weekly sampling and culture on Diamond's medium over the course of 10 months. In a 6-week test of alternative methods of diagnosis, the bulls were randomly assigned to have their preputial contents sampled weekly either by washing or by scraping of the preputial membrane. The samples were cultured on Claussen's medium and in InPouch packets at 37°C in air for 7 days. The results were compared by McNemar's χ² test for symmetry. Washing yielded 69 positive cultures from 84 samples whereas scraping yielded 65 from 83. These differences were not statistically significant. InPouch culture detected 73 of 83 samples from positive bulls, whereas Claussen's medium detected 61 of 83. The difference in sensitivity between the two culture methods was highly significant, with the InPouch method 'missing' 2 positive samples that were detected by Claussen's medium and Claussen's medium missing 14 positive samples that were detected by InPouch culture

Fast raster-scan optoacoustic mesoscopy enables assessment of human melanoma microvasculature in vivo.

Melanoma is associated with angiogenesis and vascular changes that may extend through the entire skin depth. Three-dimensional imaging of vascular characteristics in skin lesions could therefore allow diagnostic insights not available by conventional visual inspection. Raster-scan optoacoustic mesoscopy (RSOM) images microvasculature through the entire skin depth with resolutions of tens of micrometers; however, current RSOM implementations are too slow to overcome the strong breathing motions on the upper torso where melanoma lesions commonly occur. To enable high-resolution imaging of melanoma vasculature in humans, we accelerate RSOM scanning using an illumination scheme that is coaxial with a high-sensitivity ultrasound detector path, yielding 15 s single-breath-hold scans that minimize motion artifacts. We apply this Fast RSOM to image 10 melanomas and 10 benign nevi in vivo, showing marked differences between malignant and benign lesions, supporting the possibility to use biomarkers extracted from RSOM imaging of vasculature for lesion characterization to improve diagnostics

Indium sulfide thin films deposited by the spray ion layer gas reaction technique

The Spray Ion Layer Gas Reaction technique is a new variation on the ILGAR technique used to prepare chalcogenide thin films. The process involves the cyclical spray deposition of an indium containing precursor layer followed by its conversion to sulfide using hydrogen sulfide gas. High quality indium sulfide thin films are produced with an indirect bandgap of 2.2eV and a high suitability for use as buffer layers in chalcopyrite solar cells. Analysis of the deposition reveals that the indium chloride based precursor is transported via the vapour phase from the spray droplets to the substrate surfac

Genetic transformation of Knufia petricola A95 - a model organism for biofilm-material interactions

We established a protoplast-based system to transfer DNA to Knufia petricola strain A95, a melanised rock-inhabiting microcolonial fungus that is also a component of a model sub-aerial biofilm (SAB) system. To test whether the desiccation resistant, highly melanised cell walls would hinder protoplast formation, we treated a melanin-minus mutant of A95 as well as the type-strain with a variety of cell-degrading enzymes. Of the different enzymes tested, lysing enzymes from Trichoderma harzianum were most effective in producing protoplasts. This mixture was equally effective on the melanin-minus mutant and the type-strain. Protoplasts produced using lysing enzymes were mixed with polyethyleneglycol (PEG) and plasmid pCB1004 which contains the hygromycin B (HmB) phosphotransferase (hph) gene under the control of the Aspergillus nidulans trpC. Integration and expression of hph into the A95 genome conferred hygromycin resistance upon the transformants. Two weeks after plating out on selective agar containing HmB, the protoplasts developed cell-walls and formed colonies. Transformation frequencies were in the range 36 to 87 transformants per 10 μg of vector DNA and 106 protoplasts. Stability of transformation was confirmed by sub-culturing the putative transformants on selective agar containing HmB as well as by PCR-detection of the hph gene in the colonies. The hph gene was stably integrated as shown by five subsequent passages with and without selection pressure