Model and test in a fungus of the probability that beneficial mutations survive drift

Determining the probability of fixation of beneficial mutations is critically important for building predictive models of adaptive evolution. Despite considerable theoretical work, models of fixation probability have stood untested for nearly a century. However, recent advances in experimental and theoretical techniques permit the development of models with testable predictions. We developed a new model for the probability of surviving genetic drift, a major component of fixation probability, for novel beneficial mutations in the fungus Aspergillus nidulans, based on the life-history characteristics of its colony growth on a solid surface. We tested the model by measuring the probability of surviving drift in 11 adapted strains introduced into wild-type populations of different densities. We found that the probability of surviving drift increased with mutant invasion fitness, and decreased with wild-type density, as expected. The model accurately predicted the survival probability for the majority of mutants, yielding one of the first direct tests of the extinction probability of beneficial mutations.     

Computational assessment of airway wall stiffness in vivo in allergically inflamed mouse models of asthma.

Allergic inflammation is known to cause airway hyperresponsiveness in mice. However, it is not known whether inflammation affects the stiffness of the airway wall, which would alter the load against which the circumscribing smooth muscle shortens when activated. Accordingly, we measured the time course of airway resistance immediately following intravenous methacholine injection in acutely and chronically allergically inflamed mice. We estimated the effective stiffness of the airway wall in these animals by fitting to the airway resistance profiles a computational model of a dynamically narrowing airway embedded in elastic parenchyma. Effective airway wall stiffness was estimated from the model fit and was found not to change from control in either the acute or chronic inflammatory groups. However, the acutely inflamed mice were hyperresponsive compared with controls, which we interpret as reflecting increased delivery of methacholine to the airway smooth muscle through a leaky pulmonary endothelium. These results support the notion that acutely inflamed BALB/c mice represent an animal model of functionally normal airway smooth muscle in a transiently abnormal lung.     

A short-oligonucleotide microarray that allows improved detection of gastrointestinal tract microbial communities

Background  

The human gastrointestinal (GI) tract contains a diverse collection of bacteria, most of which are unculturable by conventional microbiological methods. Increasingly molecular profiling techniques are being employed to examine this complex microbial community. The purpose of this study was to develop a microarray technique based on 16S ribosomal gene sequences for rapidly monitoring the microbial population of the GI tract.     

Relationships between habitat structure and fish communities on coral

The influence of habitat structure on reef-fish communities at Bar Reef Marine Sanctuary, Sri Lanka, was investigated. The relationship between habitat characteristics and the distribution and abundance of 135 species of fishes was examined on two reef types: coral and sandstone reefs. Results suggested that the reef-fish communities were strongly influenced by various aspects of reef structure. However, relationships between habitat variables and fish communities structure, varied between the two reef types. Fish species diversity was correlated with a number of habitat variables on the sandstone reefs, although structural complexity seemed to play the dominant role. There were no correlations between habitat structure and fish diversity on the coral reefs. Total abundance was not related to any one habitat parameter on either reef type. However, abundances of some species, families and trophic groups were correlated with habitat features. These specific correlations were commonly related to food or shelter availability. For example, coral feeders were correlated with live coral cover, and pomacentrid species, which used branching corals for protection, showed a significant relationship with the density of Acropora colonies. This shows that a summary statistic such as total abundance may hide important information. Effects of habitat structure on the distribution patterns of the fish communities was further investigated using multi-dimensional scaling ordination (MDS) and the RELATE-procedure. With the MDS ordinations for both habitat and fish-community composition it was possible to show that the multivariate pattern between the two ecological components was clearly correlated.     

Expression of CD44 Splice Variants During Lymphocyte Activation and Tumor Progression

Recently, splice variants of CD44 have been described that confer metastatic potential to non-metastasizing rat pancreatic carcinoma and sarcoma cell lines. Using antibodies against variant CD44 (CD44v) sequences, we have examined the expression of variant CD44 glycoproteins on human lymphoid cells and tissues and in colorectal neoplasia. Lymphohematopoietic cells express low levels of CD44v glycoproteins. During the process of lymphocyte activation in vitro and in vivo, expression of CD44v glycoproteins is transiently upregulated. The reaction pattern of various antibodies indicates that these CD44 variants contain the domain encoded by exon v6, which is part of the variant that confers metastatic capability. In human colorectal neoplasia we observed overexpression of CD44 splice variants in all invasive carcinomas. Already at early stages of colorectal tumor progression exon v5 epitopes were overexpressed. Tumor progression was strongly related to expression of CD44 isoforms containing exon v6 encoded domains. The findings establish CD44 variants as tumor progression markers in colorectal cancer.