Acquisition of Iron by Alkaliphilic Bacillus Species

The biochemical and molecular mechanisms used by alkaliphilic bacteria to acquire iron are unknown. We demonstrate that alkaliphilic (pH > 9) Bacillus species are sensitive to artificial iron (Fe³⁺) chelators and produce iron-chelating molecules. These alkaliphilic siderophores contain catechol and hydroxamate moieties, and their synthesis is stimulated by manganese(II) salts and suppressed by FeCl₃ addition. Purification and mass spectrometric characterization of the siderophore produced by Caldalkalibacillus thermarum failed to identify any matches to previously observed fragmentation spectra of known siderophores, suggesting a novel structure.Iron is an abundant element in nature; however, in most aqueous aerobic environments iron forms insoluble ferric hydroxide, Fe(OH)₃. This poses a major problem for most aerobic bacteria, as ferric hydroxide has a solubility constant of 10⁻³⁹ M, therefore limiting the concentration of ferric ions to 10⁻¹⁸ M at pH 7.0. For example, bacteria living in seawater (approximate pH 8.0) require iron, yet dissolved iron is only present at 0.02 to 2.0 nM (5). Despite this apparent lack of bioavailability, iron has been repeatedly demonstrated to be an essential element for aerobic bacterial growth (1).With the lack of readily accessible iron at physiological pH, most bacteria have evolved systems to deal with the incumbent problem of iron acquisition. Under iron-rich conditions, Fe²⁺ uptake receptors, such as FeoAB, are synthesized in bacteria, which passively import iron in the immediate vicinity of the cell (1, 23). No equivalent system has been identified for Fe³⁺ transport. To acquire Fe³⁺ under aqueous aerobic conditions, bacteria commonly have import systems involving the synthesis, secretion, and regathering of a group of secondary metabolites known as siderophores (1, 11). Siderophores are low-molecular-weight chemical moieties that chelate Fe³⁺ and typically have complex formation (K_f) constants in the range of 10²³ to 10⁵² (11). Siderophores, like other chelators, are known to increase the solubility of iron by hindering the formation of Fe-oxyhydroxides at high pH, at which the Fe-oxyhydroxides are the dominating inorganic species (27). Siderophores are also known to facilitate the dissolution of Fe from minerals (3). Siderophore-iron complexes can either be transported through cellular membranes using dedicated transport systems or if the Fe(III) central atom is reduced, making the iron bioavailable for cellular processes (10, 14). Three major groups of siderophores have been described in bacteria: hydroxamates, catecholates, and carboxylates. Hydroxamates and catechols are commonly produced by aerobic bacteria living at neutral to alkaline pH, whereas carboxylates are significantly more common in bacteria living in mildly acidic pH (11-13). In the genus Bacillus, Bacillus megaterium and Bacillus subtilis are producers of schizokinen and bacillibactin, respectively (6, 20). Bacillus anthracis produces both a catechol and a hydroxamate siderophore (7, 34), and B. licheniformis strain VK21 is the only known example of a thermoresistant catecholate-producing Gram-positive bacterium (32).Although there is extensive literature on iron capture mechanisms in bacteria that thrive at neutral pH, there is little information at a biochemical or molecular level on how aerobic bacteria growing at extreme alkaline pHs (i.e., pH 9 to 11) acquire iron. At alkaline pH, the solubility constant for iron decreases far below the requirement for living cells, and the concentration of bioavailable iron is estimated to be approximately 10⁻²³ M at pH 10 (11). Taking this extreme lack of iron into account, the sequestering mechanisms of alkaliphilic bacteria must be powerful, yet there has been little analysis of the types of iron-chelating molecules these bacteria produce.     

Phylogenetic targeting of research effort in evolutionary biology

Many questions in comparative biology require that new data be collected, either to build a comparative database for the first time or to augment existing data. Given resource limitations in collecting data, the question arises as to which species should be studied to increase the size of comparative data sets. By taking hypotheses, existing data relevant to the hypotheses, and a phylogeny, we show that a method of “phylogenetic targeting” can systematically guide data collection while taking into account potentially confounding variables and competing hypotheses. Phylogenetic targeting selects potential candidates for future data collection, using a flexible scoring system based on differences in pairwise comparisons. We used simulations to assess the performance of phylogenetic targeting, as compared with the less systematic approach of randomly selecting species (as might occur when data have been collected without regard to phylogeny and variation in the traits of interest). The simulations revealed that phylogenetic targeting increased the statistical power to detect correlations and that power increased with the number of species in the tree, even when the number of species studied was held constant. We also developed a Web‐based computer program called PhyloTargeting to implement the approach ( http://phylotargeting.fas.harvard.edu ).     

The rise to dominance of the angiosperm kingdom: dispersal,habitat widening and evolution during the Late Cretaceous of Europe

Coiffard, C. & Gomez, B. 2009: The rise to dominance of the angiosperm kingdom: dispersal, habitat widening and evolution during the Late Cretaceous of Europe. Lethaia, Vol. 43, pp. 164–169. The earliest fossil records of angiosperms in Europe occur in the Barremian and consist of freshwater wetland plants. From the Barremian onwards, angiosperms show a stepwise widening of their ecological range with the result that they inhabited most environments by the Cenomanian. Nevertheless, most angiosperms had still restricted habitats, while a few angiosperm trees were confined to disturbed environments, such as channel margins. A Wagner’s Parsimony Method analysis performed on a fossil plant and locality database from the Turonian to the Campanian of Europe indicates continued decrease in richness of ferns and gymnosperms compared with angiosperms, turnover between conifer and palm trees in freshwater‐related swamps at about the Cenomanian/Turonian boundary, and spreading of angiosperm trees through the floodplains. The ecological range of angiosperm trees was increased, being recorded in channel margins from the Cenomanian and spreading over floodplains (e.g. Platanaceae) and swamps (e.g. Arecaceae) by the Campanian. These new ecological ranges and successions went with innovative architectures, such as dicot trees and palm trees. Most living core angiosperm families had their earliest representatives in the Late Cretaceous, which should be considered as the dawn of modern angiosperm forests. □Core angiosperms, Europe, Late Cretaceous, palms, Wagner’s Parsimony Method.     

Ranging patterns and parasitism in primates

Competing hypotheses exist concerning the influence of ranging patterns on parasitism. More intensive use of a home range could result in greater exposure to infectious agents that accumulate in the soil. Alternatively, when more intensive ranging is associated with territorial defence, this could decrease home range overlap and produce lower levels of parasitism. We tested these hypotheses using phylogenetic comparative methods and parasite richness data for 119 primate species. Helminth richness increased with the defensibility index, a quantitative measure of home range use that correlates with the degree of territoriality in primates. This association was independent of other host traits that influence parasite richness in primates. Results involving non-vector transmitted helminths produced the most significant results, suggesting that the relationship between territorial behaviour and parasitism is driven by accumulation of parasites in defended home ranges. In addition, costs associated with greater ranging could increase susceptibility to infectious agents.     

RGS17/RGSZ2 and the RZ/A family of regulators of G-protein signaling

Regulators of G-protein signaling (RGS proteins) comprise over 20 different proteins that have been classified into subfamilies on the basis of structural homology. The RZ/A family includes RGSZ2/RGS17 (the most recently discovered member of this family), GAIP/RGS19, RGSZ1/RGS20, and the RGSZ1 variant Ret-RGS. The RGS proteins are GTPase activating proteins (GAPs) that turn off G-proteins and thus negatively regulate the signaling of G-protein coupled receptors (GPCRs). In addition, some RZ/A family RGS proteins are able to modify signaling through interactions with adapter proteins (such as GIPC and GIPN). The RZ/A proteins have a simple structure that includes a conserved amino-terminal cysteine string motif, RGS box and short carboxyl-terminal, which confer GAP activity (RGS box) and the ability to undergo covalent modification and interact with other proteins (amino-terminal). This review focuses on RGS17 and its RZ/A sibling proteins and discusses the similarities and differences among these proteins in terms of their palmitoylation, phosphorylation, intracellular localization and interactions with GPCRs and adapter proteins. The specificity of these RGS protein for different Galpha proteins and receptors, and the consequences for signaling are discussed. The tissue and brain distribution, and the evolving understanding of the roles of this family of RGS proteins in receptor signaling and brain function are highlighted.     

The nucleotide sequence and deduced amino acid sequence of the cytochrome cL gene of Methylobacterium extorquens AM1, a novel class of c-type cytochrome.

The nucleotide sequence and deduced amino acid sequence of the cytochrome cL of Methylobacterium extorquens (Pseudomonas AM1; Methylobacterium AM1) shows that this cytochrome c is completely different, except for its haem-binding site, from all other cytochromes.     

Variations in the spawning periodicity of eight fish species in three English lowland rivers over a 6 year period, inferred from 0+ year fish length distributions

The spawning periodicity of eight fish species was investigated in three English lowland rivers over a 6 year period from patterns in 0+ year fish standard length ( L _S) distributions. A single cohort of 0+ year dace Leuciscus leuciscus , roach Rutilus rutilus and perch Perca fluviatilis was observed each year, suggesting that these species spawned only once annually. By contrast, populations of chub Leuciscus cephalus , bleak Alburnus alburnus , bream Abramis brama , gudgeon Gobio gobio and minnow Phoxinus phoxinus were inferred to spawn on more than one occasion each year. Annual and intercatchment variations occurred in the L _S distribution patterns of some of the fish species. In chub, for example, although a minimum of two 0+ year cohorts occurred in all years in the River Trent, 'multiple' spawning (either at the individual or population level) was most apparent in 1999, 2003 and 2004. By contrast, 'multiple' spawning events were not evident in all years in the Warwickshire Avon and Yorkshire Ouse, with recruitment presumably based upon a single spawning event in some years. There is effectively a trade-off between early spawning (extended growing season), and the possibility that environmental conditions will impact upon recruitment success, and the potential for reduced overwinter survival of smaller individuals with lower lipid resources from later spawning events. Notwithstanding, fishes as small as 15 mm L _S survived the winter in some years, suggesting that progeny from later spawning events may make important contributions to fish recruitment success.     

Parasite species richness in carnivores: effects of host body mass, latitude, geographical range and population density

Aim  Comparative studies have revealed strong links between ecological factors and the number of parasite species harboured by different hosts, but studies of different taxonomic host groups have produced inconsistent results. As a step towards understanding the general patterns of parasite species richness, we present results from a new comprehensive data base of over 7000 host–parasite combinations representing 146 species of carnivores (Mammalia: Carnivora) and 980 species of parasites.
Methods  We used both phylogenetic and non-phylogenetic comparative methods while controlling for unequal sampling effort within a multivariate framework to ascertain the main determinants of parasite species richness in carnivores.
Results  We found that body mass, population density, geographical range size and distance from the equator are correlated with overall parasite species richness in fissiped carnivores. When parasites are classified by transmission mode, body mass and home range area are the main determinants of the richness of parasites spread by close contact between hosts, and population density, geographical range size and distance from the equator account for the diversity of parasites that are not dependent on close contact. For generalist parasites, population density, geographical range size and latitude are the primary predictors of parasite species richness. We found no significant ecological correlates for the richness of specialist or vector-borne parasites.
Main conclusions  Although we found that parasite species richness increases instead of decreases with distance from the equator, other comparative patterns in carnivores support previous findings in primates, suggesting that similar ecological factors operate in both these independent evolutionary lineages.     

Comparative tests of parasite species richness in primates

Some hosts harbor diverse parasite communities, whereas others are relatively parasite free. Many factors have been proposed to account for patterns of parasite species richness, but few studies have investigated competing hypotheses among multiple parasite communities in the same host clade. We used a comparative data set of 941 host-parasite combinations, representing 101 anthropoid primate species and 231 parasite taxa, to test the relative importance of four sets of variables that have been proposed as determinants of parasite community diversity in primates: host body mass and life history, social contact and population density, diet, and habitat diversity. We defined parasites broadly to include not only parasitic helminths and arthropods but also viruses, bacteria, fungi, and protozoa, and we controlled for effects of uneven sampling effort on per-host measures of parasite diversity. In nonphylogenetic tests, body mass was correlated with total parasite diversity and the diversity of helminths and viruses. When phylogeny was taken into account, however, body mass became nonsignificant. Host population density, a key determinant of parasite spread in many epidemiological models, was associated consistently with total parasite species richness and the diversity of helminths, protozoa, and viruses tested separately. Geographic range size and day range length explained significant variation in the diversity of viruses.