Extracytoplasmic Stress Responses Induced by Antimicrobial Cationic Polyethylenimines

The ability of an antimicrobial, cationic polyethylenimine (PEI+) to induce the three known extracytoplasmic stress responses of Escherichia coli was quantified. Exposure of E. coli to PEI+ in solution revealed specific, concentration-dependent induction of the Cpx extracytoplasmic cellular stress response, ~2.0–2.5-fold at 320?μg/mL after 1.5?h without significant induction of the σ^E or Bae stress responses. In comparison, exposure of E. coli to a non-antimicrobial polymer, poly(ethylene oxide) (PEO), resulted in no induction of the three stress responses. The antimicrobial small molecule vanillin, a known membrane pore-forming compound, was observed to cause specific, concentration-dependent induction of the σ^E stress response, ~6-fold at 640?μg/mL after 1.5?h, without significant induction of the Cpx or Bae stress responses. The different stress response induction profiles of PEI+ and vanillin suggest that although both are antimicrobial compounds, they interact with the bacterial membrane and extracytoplasmic area by unique mechanisms. EPR studies of liposomes containing spin-labeled lipids exposed to PEI+, vanillin, and PEO reveal that PEI+ and PEO increased membrane stability, whereas vanillin was found to have no effect.     

Genomic and functional analysis of Vibrio phage SIO-2 reveals novel insights into ecology and evolution of marine siphoviruses

We report on a genomic and functional analysis of a novel marine siphovirus, the Vibrio phage SIO-2. This phage is lytic for related Vibrio species of great ecological interest including the broadly antagonistic bacterium Vibrio sp. SWAT3 as well as notable members of the Harveyi clade (V.harveyi ATTC BAA-1116 and V.campbellii ATCC 25920). Vibrio phage SIO-2 has a circularly permuted genome of 80598 bp, which displays unusual features. This genome is larger than that of most known siphoviruses and only 38 of the 116 predicted proteins had homologues in databases. Another divergence is manifest by the origin of core genes, most of which share robust similarities with unrelated viruses and bacteria spanning a wide range of phyla. These core genes are arranged in the same order as in most bacteriophages but they are unusually interspaced at two places with insertions of DNA comprising a high density of uncharacterized genes. The acquisition of these DNA inserts is associated with morphological variation of SIO-2 capsid, which assembles as a large (80 nm) shell with a novel T=12 symmetry. These atypical structural features confer on SIO-2 a remarkable stability to a variety of physical, chemical and environmental factors. Given this high level of functional and genomic novelty, SIO-2 emerges as a model of considerable interest in ecological and evolutionary studies.     

Assisted assembly: how to improve a de novo genome assembly by using related species

We describe a new assembly algorithm, where a genome assembly with low sequence coverage, either throughout the genome or locally, due to cloning bias, is considerably improved through an assisting process via a related genome. We show that the information provided by aligning the whole-genome shotgun reads of the target against a reference genome can be used to substantially improve the quality of the resulting assembly.     

Anteroposterior patterning in hemichordates and the origins of the chordate nervous system

The chordate central nervous system has been hypothesized to originate from either a dorsal centralized, or a ventral centralized, or a noncentralized nervous system of a deuterostome ancestor. In an effort to resolve these issues, we examined the hemichordate Saccoglossus kowalevskii and studied the expression of orthologs of genes that are involved in patterning the chordate central nervous system. All 22 orthologs studied are expressed in the ectoderm in an anteroposterior arrangement nearly identical to that found in chordates. Domain topography is conserved between hemichordates and chordates despite the fact that hemichordates have a diffuse nerve net, whereas chordates have a centralized system. We propose that the deuterostome ancestor may have had a diffuse nervous system, which was later centralized during the evolution of the chordate lineage.     

SUBCELLULAR DISTRIBUTION OF DOPAMINE-β-HYDROXYLASE AND INHIBITORS IN THE HIPPOCAMPUS AND CAUDATE NUCLEUS IN SHEEP BRAIN

—The enzyme dopamine-β-hydroxylase (EC 1.14.17.1) which converts dopamine to noradrenaline was found to be present in substantial amounts in sheep brain hypothalamus and caudate nucleus and was located to the synaptic vesicle fractions in these two brain regions by subcellular fractionation. This dopamine-β-hydroxylase was associated with paniculate matter in these two brain regions since it was resistant to solubilization with butan-1-ol and 0.1% Triton X-100. As highly significant levels of dopamine-β-hydroxylase were present in the caudate nucleus, factors other than a simple lack of this enzyme must operate to maintain the low levels of noradrenaline and high levels of dopamine in the caudate nucleus. Purified adrenal dopamine-β-hydroxylase was substantially inhibited by two factors prepared from sheep brain hypothalamus and caudate nucleus. These were found to be cupric ions and a sulphydryl inhibitor. High levels of the sulphydryl inhibitor of dopamine-β-hydroxylase were found in synaptosomal fractions from sheep brain hypothalamus and caudate nucleus and the levels were comparable in both regions. Upon subfractionation of a synaptosome-containing fraction from the hypothalamus, the inhibitor was located predominantly in the soluble fraction, although there were significant levels in the synaptic vesicle fraction. Therefore, the sulphydryl inhibitor must be considered as a possible regulator of dopamine-β-hydroxylase activity. Free cupric ion concentrations as low as 2·5 μM were found to inhibit purified adrenal dopamine-β-hydroxylase in vitro and the concentration of copper in the soluble tissue component of hypothalamus and caudate nucleus was well above this minimal copper concentration. The percentage content of soluble copper in the caudate nucleus was significantly higher than in the hypothalamus. The importance of the soluble to particulate-bound ratio of copper in brain was shown in studies of the developing rat brain. A rapid increase in the level of copper in brain was found in the first 4 weeks but the level was constant by 2 months of age. The percentage of soluble copper, however, was maximal soon after birth and had declined to a constant figure by 2 months of age. A scheme for the regulation of dopamine-β-hydroxylase activity involving these factors is proposed.     

Support for the habitat amount hypothesis from a global synthesis of species density studies

Decades of research suggest that species richness depends on spatial characteristics of habitat patches, especially their size and isolation. In contrast, the habitat amount hypothesis predicts that (1) species richness in plots of fixed size (species density) is more strongly and positively related to the amount of habitat around the plot than to patch size or isolation; (2) habitat amount better predicts species density than patch size and isolation combined, (3) there is no effect of habitat fragmentation per se on species density and (4) patch size and isolation effects do not become stronger with declining habitat amount. Data on eight taxonomic groups from 35 studies around the world support these predictions. Conserving species density requires minimising habitat loss, irrespective of the configuration of the patches in which that habitat is contained.     

The Circe principle explains how resource-rich land can waylay pollinators in fragmented landscapes

Global declines in pollinators, associated with land-use change [1-6] and fragmentation [7-10], constitute a serious threat to crop production and biodiversity [11]. Models investigating impacts of habitat fragmentation on pollen flow have categorized landscapes simply in terms of habitat and nonhabitat. We show that pollen flow depends strongly on types of land use between habitat fragments. We used paternity analysis of seeds and a combination of circuit and general linear models to analyze pollen flow for the endangered tree Gomortega keule (Gomortegaceae) [12] in the fragmented Central Chile Biodiversity Hotspot [13]. Pollination probability was highest over pine plantation, moderate over low-intensity agriculture and native forest, and lowest over clearfells. Changing the proportions of the land uses over one kilometer altered pollination probability up to 7-fold. We explain our results by the novel "Circe principle." In contrast to models where land uses similar to native habitat promote pollinator movement, pollinators may actually be waylaid in resource-rich areas between habitat patches. Moreover, pollinators may move with higher probability between habitat patches separated by some resource-poor land uses. Pollination research in fragmented landscapes requires explicit recognition of the nature of the nonhabitat matrix, rather than applying simple binary landscape models.     

Spatiotemporal mechanisms of morphogen gradient interpretation

Few mechanistic ideas from the pre-molecular era of biology have had as enduring an impact as the morphogen concept. In the classical view, cells in developing embryos obtain positional information by measuring morphogen concentrations and comparing them with fixed concentration thresholds; as a result, graded morphogen distributions map into discrete spatial arrangements of gene expression. Recent studies on Hedgehog and other morphogens suggest that establishing patterns of gene expression may be less a function of absolute morphogen concentrations, than of the dynamics of signal transduction, gene expression, and gradient formation. The data point away from any universal model of morphogen interpretation and suggest that organisms use multiple mechanisms for reading out developmental signals in order to accomplish specific patterning goals.