Identifying essential genes in bacterial metabolic networks with machine learning methods

Background  

Identifying essential genes in bacteria supports to identify potential drug targets and an understanding of minimal requirements for a synthetic cell. However, experimentally assaying the essentiality of their coding genes is resource intensive and not feasible for all bacterial organisms, in particular if they are infective.     

The development of anoxia following occlusion

Following arteriolar occlusion, tissue oxygen concentration decreases and anoxic tissue eventually develops. Although anoxia first appears in the region most distal to the capillary at the venous end, it eventually spreads throughout the entire region of supply. In this paper the changing oxygen concentration, from the time of occlusion until the tissue is entirely anoxic, is examined mathematically. The equations governing oxygen transport to tissue are solved by iterating a nonlinear integral equation. This solution is valid until anoxia first appears. After anoxia develops it is necessary to solve a moving boundary problem. This is done using the method of matched asymptotic expansions, and accurate solutions are obtained for a wide range of physiological conditions.     

Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins

Background  

Phylogenies capture the evolutionary ancestry linking extant species. Correlations and similarities among a set of species are mediated by and need to be understood in terms of the phylogenic tree. In a similar way it has been argued that biological networks also induce correlations among sets of interacting genes or their protein products.     

Membrane microheterogeneity: Förster resonance energy transfer characterization of lateral membrane domains

Lateral membrane heterogeneity, in the form of lipid rafts and microdomains, is currently implicated in cell processes including signal transduction, endocytosis, and cholesterol trafficking. Various biophysical techniques have been used to detect and characterize lateral membrane domains. Among these, Förster resonance energy transfer (FRET) has the crucial advantage of being sensitive to domain sizes smaller than 50-100 nm, below the resolution of optical microscopy but, apparently, similar to those of rafts in cell membranes. In the last decade, several formalisms for the analysis of FRET in heterogeneous membrane systems have been derived and applied to the study of microdomains. They are critically described and illustrated here.     

Boring Forminifera in French Polynesian coral reefs

The discovery of epipsammitic Foraminifera in sediments of Moorea and Scilly (French Polynesia) and the study of close relationships between embedded specimens and host-grains indicate that some species participate in the weakening and subsequent breakdown of skeletal grains and consequently contribute to the production of silt-sized particles. The study of 36 stations around the islands shows the factors that control the distribution and abundance of this incrusted microfauna. Specimens are more abundant on sand particles larger than 1,000 microns and in the high energy areas; this abundance decreases with depth. The physiological mechanism of penetrations is presumably chemical, but each species apparently has its own process: complete dissolution with removal of ions for the cytoplasm of calcareous species; partial dissolution with transport of silt-size aggregates on the test of agglutinated species. The purpose of such penetration may be to protect themselves against water turbulence and to provide material for test construction.