The contribution of common and rare species to plant species richness patterns: the effect of habitat type and size of sampling unit

Understanding how overall patterns of spatial variation in species richness are affected by distributional patterns of species has been an area of growing concern. In the present study, we investigated the relative importance of common and rare species as contributors in overall plant species richness. We further examined if the effects of common or rare species in richness patterns are affected by the size of the sampling units and if the observed patterns hold at different habitats. We used a dataset of 5,148 higher plant species distributed across 16,114 sampling plots located in 240 sites of the NATURA 2000 network of Greece. We ranked all species based on the number of sites they occupied and we developed a common to rare and a rare to common sequence. We correlated those sequences with cumulative species distributions. We performed this analysis in nine different sizes of sampling units and in three different datasets referring to (a) all habitat types together, (b) coniferous habitats only and (c) alpine habitats only. Our analysis showed that despite the proportionally higher numbers of restricted species, widespread species make a greater contribution to overall richness patterns and that this observed pattern does not depend on the size of the sampling units. Moreover, the observed pattern stands for different habitat types. Our findings support the generality of this pattern and highlight the importance of widespread species as adequate indicators of biodiversity patterns at various habitat types. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Nitrosyliron(III) hemoglobin: autoreduction and spectroscopy

Nitrosyl complexes of the iron(III) forms of myoglobin, human hemoglobin, Glycera dibranchiata hemoglobins (Hbm and Hbh), and model iron(II) and iron(III) synthetic porphyrins including octaethylporphyrin (OEP) have been prepared. The iron(III) heme proteins are electron spin (paramagnetic) resonance (ESR) silent, while hexacoordinate solution structures are indicated for [Fe(OEP)(NO)2]ClO4 and for Hbm(II)NO, which has an ESR spectrum similar to that of Mb(II)NO and the hexacoordinate iron(II) model complex Fe(OEP)NO(BzIm). The splitting of the alpha- and beta-bands in the optical spectrum of Mb(III)NO and Hbh(III)NO contrasts markedly with the sharp, single bands observed in that of Hbm-(III)NO. The nondegeneracy of the dxz and dyz orbitals in Mb(III)NO and Hbh(III)NO is attributed to the influence of the distal histidine. Circular dichroism spectra were obtained for Hbm(III)NO, Hbm(II)NO, Hbh(III)NO, Hbh(II)NO, Mb(II)NO, and Mb(III)NO. The vicinal chiral center contribution that governs the heme protein CD leads to low Kuhn anisotropies, which have been used to assign certain electronic transitions. The Hb(III)NO spectrum is not stable but transforms into that of Hb(II)NO. This autoredox process follows kinetics that are first order in FeIIINO. The relative rates of autoreduction (25 degrees C, 1 atm NO) are Mb(III)NO less than Hbm(III)NO less than Hb alpha(III)NO less than HbA(III)NO. At high NO partial pressure or after "recycling" of HbA, the rates of reduction decrease. The first step in the reaction of NO with the ferric heme is the reversible formation of the formally iron(III) adduct. This reacts with another molecule of NO, generating the final heme(II)-NO via nitrosylation of NO itself or of an endogenous nucleophile. Kinetic and spectroscopic evidence shows involvement of trans-heme-(NO)2 in the reaction. The activation parameters delta H and delta S were determined. The overall reaction is photoenhanced.     

11beta-hydroxysteroid dehydrogenase functions reversibly as an oxidoreductase in the rat hippocampus in vivo

The localization in the brain and metabolism of 3H-labeled corticosterone (B) and 11-dehydrocorticosterone (A) of high specific radioactivity was determined after stereotaxic injection into the hippocampus of anesthetized rats. [3H]B was cleared very rapidly with, on average, only about 7% being recovered after 5 min and 0.5% after 30 min. Most of this 3H-radioactivity was localized in the area surrounding the site of injection with little diffusion to adjacent areas. These findings make it possible to compare the short term metabolism of [3H]A and [3H]B in different lobes of the hippocampus in the same animal and establish their local equilibrium point in vivo. Under these conditions, about 5% conversion of each steroid to the other was observed in contrast to the situation in cultured hippocampal cells where 11beta-hydroxysteroid dehydrogenase (11-HSD) has been shown by others to act primarily as a reductase catalyzing the conversion of A to B. This method can also be used to study the effect of inhibitors such as 11alpha-hydroxyprogesterone, applied locally in the brain, on the metabolism of corticosteroids. The rate of conversion [3H]B or [3H]A to their dihydro- and tetrahydro-derivatives capable of modulating the GABAa receptor in the hippocampus was much lower than their interconversion. Thus, factors which influence the direction of the 11-HSD catalyzed reaction are important in regulating not only salt appetite and blood pressure but also the levels of neuroactive metabolites of corticosterone.     

Characterization of Aquifex aeolicus 4-diphosphocytidyl-2C-methyl-d-erythritol kinase - ligand recognition in a template for antimicrobial drug discovery

4-Diphosphocytidyl-2C-methyl-D-erythritol kinase (IspE) catalyses the ATP-dependent conversion of 4-diphosphocytidyl-2C-methyl-D-erythritol (CDPME) to 4-diphosphocytidyl-2C-methyl-d-erythritol 2-phosphate with the release of ADP. This reaction occurs in the non-mevalonate pathway of isoprenoid precursor biosynthesis and because it is essential in important microbial pathogens and absent from mammals it represents a potential target for anti-infective drugs. We set out to characterize the biochemical properties, determinants of molecular recognition and reactivity of IspE and report the cloning and purification of recombinant Aquifex aeolicus IspE (AaIspE), kinetic data, metal ion, temperature and pH dependence, crystallization and structure determination of the enzyme in complex with CDP, CDPME and ADP. In addition, 4-fluoro-3,5-dihydroxy-4-methylpent-1-enylphosphonic acid (compound 1) was designed to mimic a fragment of the substrate, a synthetic route to 1 was elucidated and the complex structure determined. Surprisingly, this ligand occupies the binding site for the ATP alpha-phosphate not the binding site for the methyl-D-erythritol moiety of CDPME. Gel filtration and analytical ultracentrifugation indicate that AaIspE is a monomer in solution. The enzyme displays the characteristic alpha/beta galacto-homoserine-mevalonate-phosphomevalonate kinase fold, with the catalytic centre positioned in a deep cleft between the ATP- and CDPME-binding domains. Comparisons indicate a high degree of sequence conservation on the IspE active site across bacterial species, similarities in structure, specificity of substrate recognition and mechanism. The biochemical characterization, attainment of well-ordered and reproducible crystals and the models resulting from the analyses provide reagents and templates to support the structure-based design of broad-spectrum antimicrobial agents.     

Discovery of novel Jak2–Stat pathway inhibitors with extended residence time on target

The discovery of the activating mutation V617F in the JH2 domain of Jak2 and the modulation of oncogenic Stat3 by Jak2 inhibitors have spurred a great interest in the inhibition of the Jak2/Stat pathway in oncology. In this Letter, we communicate the discovery of novel inhibitors of the Jak2/Stat5 axis, the N-(1H-pyrazol-3-yl)pyrimidin-2-amino derivatives. The rationale, synthesis and biological evaluation of these derivatives are reported. Two lead analogs from this series, 6 and 9, displayed prolonged residence time on Jak2, at enzymatic level. Although 6 and 9 exhibited moderate selectivity in a selected kinase panel, we chose to test these inhibitors in vivo as a consequence to their long residence time. However, extended inhibition of Jak2 due to the long residence time, in the form of inhibiting phosphorylation of downstream Stat5, was not recapitulated in an in vivo setting.     

Spectroscopic and kinetic aspects of Elephas maximus hemoglobin

In comparison with myoglobin and human and Glycera dibranchiata hemoglobins, the heme distal side amino acid exchanges within the heme environment of elephant tetrameric hemoglobin (Hbe) only slightly affect the electronic and ESR spectra of Hbe(III) and Hbe(II) derivatives, several of which were prepared and characterized by optical and ESR spectroscopy. Addition of 2,3-bisphosphoglycerate [Gri(2,3)P2] or inositol hexakisphosphate to Hbe(II)NO causes tension in the Fe-N(proximal His) bond, although the behaviour differs in detail from that of HbA(II)NO. There are two equilibrium states of Hbe having significantly different kinetics for the Hbe(III)----Hbe(II) reaction of Hbe(III)NO. This autoreduction occurs in the form of two parallel processes, which collapse into one intermediate rate in the presence of Gri(2,3)P2. The temperature dependences of the rates enable deduction of delta H0 and delta S0 for the linked equilibrium, and yield linear Eyring plots for Hbe(III)NO, from which activation parameters were estimated on the basis of a previously described mechanism.     

Rusty, jammed, and well-oiled hinges: Mutations affecting the interdomain region of FliG, a rotor element of the Escherichia coli flagellar motor

The FliG protein is a central component of the bacterial flagellar motor. It is one of the first proteins added during assembly of the flagellar basal body, and there are 26 copies per motor. FliG interacts directly with the Mot protein complex of the stator to generate torque, and it is a crucial player in switching the direction of flagellar rotation from clockwise (CW) to counterclockwise and vice versa. A primarily helical linker joins the N-terminal assembly domain of FliG, which is firmly attached to the FliF protein of the MS ring of the basal body, to the motility domain that interacts with MotA/MotB. We report here the results of a mutagenic analysis focused on what has been called the hinge region of the linker. Residue substitutions in this region generate a diversity of phenotypes, including motors that are strongly CW biased, infrequent switchers, rapid switchers, and transiently or permanently paused. Isolation of these mutants was facilitated by a "sensitizing" mutation (E232G) outside of the hinge region that was accidentally introduced during cloning of the chromosomal fliG gene into our vector plasmid. This mutation partially interferes with flagellar assembly and accentuates the defects associated with mutations that by themselves have little phenotypic consequence. The effects of these mutations are analyzed in the context of a conformational-coupling model for motor switching and with respect to the structure of the C-terminal 70% of FliG from Thermotoga maritima.