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Previous phylogenetic analyses revealed that species within the genera Nimbya and Embellisia reside within a large monophyletic clade that also includes the genera Alternaria, Ulocladium, Undifilum, Sinomyces, and Crivellia with Stemphylium as the sister taxon. This study expands upon previous work by including many contemporary species of each genus and(More)
We present a new method to fit grammar-based stochas-tic models for biological structure to stacks of microscopic images captured at incremental focal lengths. Providing the ability to quantitatively represent structure and automatically fit it to image data enables important biological research. We consider the case where individuals can be represented as(More)
Nonribosomal peptides (NRPs) and polyketides (PKs) are ecologically important secondary metabolites produced by bacteria and fungi using multidomain enzymes called nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), respectively. Previous phylogenetic analyses of fungal NRPSs and PKSs have suggested that a few of these genes were(More)
Caves are relatively accessible subterranean habitats ideal for the study of subsurface microbial dynamics and metabolisms under oligotrophic, non-photosynthetic conditions. A 454-pyrotag analysis of the V6 region of the 16S rRNA gene was used to systematically evaluate the bacterial diversity of ten cave surfaces within Kartchner Caverns, a limestone cave.(More)
The infectoria species-group within the genus Alternaria was originally conceived by Simmons in 1993 and was based upon common morphological characteristics that included the development of conidial chains with primary, secondary, and tertiary branching resulting in substantial three-dimensional complexity. These characters can overlap to varying degrees(More)
Research on the distribution and structure of fungal communities in caves is lacking. Kartchner Caverns is a wet and mineralogically diverse carbonate cave located in an escarpment of Mississippian Escabrosa limestone in the Whetstone Mountains, Arizona, USA. Fungal diversity from speleothem and rock wall surfaces was examined with 454 FLX Titanium(More)
We present a novel method for detecting and quantifying 3D structure in stacks of microscopic images captured at incremental focal lengths. We express the image data as stochastically generated by an underlying model for biological specimen and the effects of the imaging system. The method simultaneously fits a model for proposed structure and the imaging(More)
In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: Modelling Morphology Morphometrics a b s t r a c t Alternaria is one of the most(More)
An improved procedure for preparing PCR cloning vectors was developed. This procedure includes the incorporation of adapters to create XcmI restriction enzyme sites in pBluescript II SK(+) vectors, digestion with XcmI followed by further digestion of the small fragment produced by XcmI digestion with additional enzymes, and purification with PCR(More)
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