Biosynthesis of (10R)-Juvenile hormone III from farnesoic acid by Aedes aegypti ovary

Synthesis of (10R)-juvenile hormone III (JH III) outside the corpora allata (CA) was investigated in female Aedes aegypti. Intact females or ligated abdomens of blood-fed and sugar-fed females synthesized in vivo [12-³H]JH III-like molecules from [12-³H]-methyl farnesoate, indicating that an organ(s) in the female abdomen, other than the CA, converted methyl farnesoate into JH III. To find out the organ(s) that synthesized JH III-like molecules, ovaries, fat bodies, and midguts were incubated in vitro with [12-³H]methyl farnesoate and the synthesis of JH III-like molecules was compared with JH III synthesized by CA. To identify tissue(s) having both farnesoic acid methyl transferase and farnesoate epoxidase, enzymes that convert farnesoic acid into JH III, ovaries, and fat bodies were removed from sugar and blood-fed females and incubated with [12-³H]farnesoic acid. Chemical derivatization by methoxyhydrin formation followed by esterification with (+)-α-methoxy- α-trifluoromethyl phenylacetic (MTPA) acid chloride and reversed phase liquid chromatography identified (10R)-JH III methoxyhydrin (+)-MTPA ester as the sole JH III-like molecule produced in tissue culture incubation of ovaries. Since only (10R)-JH III is produced and not racemic JH III, the oxidation of farnesoic acid must be enzymatically mediated. Ovaries and corpora allata of female A. aegypti also synthesized [³H,¹⁴C]JH III from L-[methyl-³H]methionine and [¹⁴C]acetate which was characterized by HPLC and gas chromatography. These results suggest that mosquito ovary can synthesize (10R)-JH III from farnesoic acid, and that this tissue synthesizes JH III-like molecules from L-methionine and acetate. © 1994 Wiley-Liss, Inc.     

Carbon regulation of environmental pH by secreted small molecules that modulate pathogenicity in phytopathogenic fungi

Fruit pathogens can contribute to the acidification or alkalinization of the host environment. This capability has been used to divide fungal pathogens into acidifying and/or alkalinizing classes. Here, we show that diverse classes of fungal pathogens—Colletotrichum gloeosporioides, Penicillium expansum, Aspergillus nidulans and Fusarium oxysporum—secrete small pH‐affecting molecules. These molecules modify the environmental pH, which dictates acidic or alkaline colonizing strategies, and induce the expression of PACC‐dependent genes. We show that, in many organisms, acidification is induced under carbon excess, i.e. 175 mm sucrose (the most abundant sugar in fruits). In contrast, alkalinization occurs under conditions of carbon deprivation, i.e. less than 15 mm sucrose. The carbon source is metabolized by glucose oxidase (gox2) to gluconic acid, contributing to medium acidification, whereas catalysed deamination of non‐preferred carbon sources, such as the amino acid glutamate, by glutamate dehydrogenase 2 (gdh2), results in the secretion of ammonia. Functional analyses of Δgdh2 mutants showed reduced alkalinization and pathogenicity during growth under carbon deprivation, but not in high‐carbon medium or on fruit rich in sugar, whereas analysis of Δgox2 mutants showed reduced acidification and pathogencity under conditions of excess carbon. The induction pattern of gdh2 was negatively correlated with the expression of the zinc finger global carbon catabolite repressor creA. The present results indicate that differential pH modulation by fruit fungal pathogens is a host‐dependent mechanism, affected by host sugar content, that modulates environmental pH to enhance fruit colonization.     

Seed rain and environmental controls on invasion of <Emphasis Type="Italic">Picea abies</Emphasis> into grassland

Although changes in land-use, climate, and the spread of introduced tree species have increased the global importance of tree invasions into grasslands, our ability to predict any particular invasion is limited. To elucidate mechanisms driving tree invasions of grasslands, we studied in detail how seed dispersal and fine-scale environment control the expansion of an introduced Picea abies Karst. (Norway spruce) population into Western Carpathian grassland. We mapped invading trees and measured tree size, fecundity, seed rain, seedling density, plant community composition, and light and soil environment within a 200 × 60 m belt across the invasion front. Maximum likelihood estimates of dispersal kernels suggested peak seed deposition directly underneath tree crowns where germination was poor, but mean dispersal distances were sufficiently large to generate overlapping seed shadows from multiple trees that saturated the invasion front with seeds further away from seed-dispersing trees. Partial Mantel tests indicated that germinant density was affected considerably less by seed rain than by moss cover (r = 0.54), overstory tree influence (r = −0.32), soil moisture (r = 0.21), grass cover (r = −0.15), and diffuse radiation (r = 0.13). However, these variables were not independent but formed complex multivariate gradients within the invasion front. Moss cover and soil moisture were negatively correlated with overstory tree influence and the resulting gradient clearly affected germinant density (partial Mantel r = 0.45). In contrast, positively correlated light and grass cover defined a gradient related weakly to germinant density (partial Mantel r = 0.05) as it integrated opposing effects of these variables on germinants. Seedlings had similar environmental associations, but except for the lasting positive effects of moss these tended to weaken with seedling size. Although a few seedlings may establish and survive in the more adverse environment of the outer edges of the invasion front, a significant population expansion may require a gradual build-up of the critical density of invading trees to reduce grass cover and facilitate germination on moist mossy seedbeds within uncolonized areas. Thus, Picea abies appears more likely to spread within temperate grasslands by gradual expansion of its population frontier rather than by advanced groups.     

Bridging structural biology and genomics: assessing protein interaction data with known complexes

Currently, there is a major effort to map protein-protein interactions on a genome-wide scale. The utility of the resulting interaction networks will depend on the reliability of the experimental methods and the coverage of the approaches. Known macromolecular complexes provide a defined and objective set of protein interactions with which to compare biochemical and genetic data for validation. Here, we show that a significant fraction of the protein-protein interactions in genome-wide datasets, as well as many of the individual interactions reported in the literature, are inconsistent with the known 3D structures of three recent complexes (RNA polymerase II, Arp2/3 and the proteasome). Furthermore, comparison among genome-wide datasets, and between them and a larger (but less well resolved) group of 174 complexes, also shows marked inconsistencies. Finally, individual interaction datasets, being inherently noisy, are best used when integrated together, and we show how simple Bayesian approaches can combine them, significantly decreasing error rate.     

Flexibility versus “rigidity” of the functional architecture of AChE active center

Functional architecture of the AChE active center appears to be characterized by both structural “rigidity”, necessary to stabilize the catalytic triad as well as by flexibility in accommodating the different, high affinity AChE ligands. These seemingly conflicting structural properties of the active center are demonstrated through combination of structural methods with kinetic studies of the enzyme and its mutant derivatives with plethora of structurally diverse ligands and in particular with series of stereoselective covalent and noncovalent AChE ligands. Thus, steric perturbation of the acyl pocket precipitates in a pronounced stereoselectivity toward methylphosphonates by disrupting the stabilizing environment of the catalytic histidine rather than through steric exclusion demonstrating the functional importance of the “rigid” environment of the catalytic machinery. The acyl pocket, the cation-binding subsite (Trp86) and the peripheral anionic subsite were also found to be directly involved in HuAChE stereoselectivity toward charged chiral phosphonates, operating through differential positioning of the ligand cationic moiety within the active center. Residue Trp86 is also a part of the “hydrophobic patch” which seems flexible enough to accommodate the structurally diverse ligands like tacrine, galanthamine and the two diastereomers of huperzine A. Also, we have recently discovered further aspects of the role of both the unique structure and the flexibility of the “hydrophobic patch” in determining the reactivity and stereoselectivity of HuAChE toward certain carbamates including analogs of physostigmine. In these cases the ligands are accommodated mostly through hydrophobic interactions and their stereoselectivity delineates precisely the steric limits of the pocket. Hence, the HuAChE stereoselectivity provides a sensitive tool in the in depth exploration of the functional architecture of the active center. These studies suggest that the combination of “rigidity” and flexibility within the HuAChE gorge are an essential element of its molecular design.     

Accommodation of physostigmine and its analogues by acetylcholinesterase is dominated by hydrophobic interactions

The role of the functional architecture of the HuAChE (human acetylcholinesterase) in reactivity toward the carbamates pyridostigmine, rivastigmine and several analogues of physostigmine, that are currently used or considered for use as drugs for Alzheimer's disease, was analysed using over 20 mutants of residues that constitute the interaction subsites in the active centre. Both steps of the HuAChE carbamylation reaction, formation of the Michaelis complex as well as the nucleophilic process, are sensitive to accommodation of the ligand by the enzyme. For certain carbamate/HuAChE combinations, the mode of inhibition shifted from a covalent to a noncovalent type, according to the balance between dissociation and covalent reaction rates. Whereas the charged moieties of pyridostigmine and rivastigmine contribute significantly to the stability of the corresponding HuAChE complexes, no such effect was observed for physostigmine and its analogues, phenserine and cymserine. Moreover, physostigmine-like ligands carrying oxygen instead of nitrogen at position -1 of the tricyclic moiety (physovenine and tetrahydrofurobenzofuran analogues) displayed comparable structure-function characteristics toward the various HuAChE enzymes. The essential role of the HuAChE hydrophobic pocket, comprising mostly residues Trp(86) and Tyr(337), in accommodating (-)-physostigmine and in conferring approximately 300-fold stereoselectivity toward physostigmines, was elucidated through examination of the reactivity of selected HuAChE mutations toward enantiomeric pairs of different physostigmine analogues. The present study demonstrates that certain charged and uncharged ligands, like analogues of physostigmine and physovenine, seem to be accommodated by the enzyme mostly through hydrophobic interactions.     

Plants intertwine fluvial landform dynamics with ecological succession and natural selection: a niche construction perspective for riparian systems

Aim   To contribute to the development of a macroevolutionary framework for riparian systems, reinforcing conceptual linkages between earth surface processes and biological and ecological processes.
Location   Riparian systems.
Methods   Literature review leading to an original proposition for perceiving the functioning of riparian systems in a new and different way.
Results   Riparian systems provide diverse landforms, habitats and resources for animals and plants. Certain organisms, defined as 'ecosystem engineers', significantly create and modify the physical components of riparian systems. Many studies have highlighted such engineering effects by animals on riparian systems, but the identification and understanding of the effects and responses of plants within fluvial corridors have emerged only recently. The modulation of matter, resources and energy flows by engineering plants helps establish characteristic sequences of fluvial landform creation and maintenance associated with synergetic ecological successions. We relate this process to the concept of niche construction, developed mainly by evolutionary biologists. Feedbacks between adaptive responses of riparian plants to flow regime and adjusting effects on biostabilization and bioconstruction are discussed in the context of niche construction at the scale of ecological succession and the evolution of organisms.
Main conclusions   Our conceptualization forges an integrated approach for understanding vegetated fluvial systems from a macroevolutionary perspective, for elucidating riparian ecosystem dynamics and potentially for establishing long-term stream conservation and restoration strategies.     

The paradox of invasion

It is paradoxical that exotic species invade and displace native species that are well adapted to local environments. Yet, even those exotics that eventually become abundant and widespread, often do so only after having failed to establish following multiple earlier introductions. The first pattern, while not generally discussed in this context, is usually explained by exotic species pre‐adaptations for human‐altered environments and by a release from enemies. It can be understood further by examining the superior quality of colonists from large species‐rich regions and the historical contingency of evolution. The second pattern is generally explained by invoking demographic and environmental stochasticity; however, it can be understood further by examining the role of environmental variation over space and by metapopulation dynamics. These processes provide a context in which these patterns of invasion are not paradoxical, but instead, expected.     

Genomics and privacy: implications of the new reality of closed data for the field

Open source and open data have been driving forces in bioinformatics in the past. However, privacy concerns may soon change the landscape, limiting future access to important data sets, including personal genomics data. Here we survey this situation in some detail, describing, in particular, how the large scale of the data from personal genomic sequencing makes it especially hard to share data, exacerbating the privacy problem. We also go over various aspects of genomic privacy: first, there is basic identifiability of subjects having their genome sequenced. However, even for individuals who have consented to be identified, there is the prospect of very detailed future characterization of their genotype, which, unanticipated at the time of their consent, may be more personal and invasive than the release of their medical records. We go over various computational strategies for dealing with the issue of genomic privacy. One can "slice" and reformat datasets to allow them to be partially shared while securing the most private variants. This is particularly applicable to functional genomics information, which can be largely processed without variant information. For handling the most private data there are a number of legal and technological approaches-for example, modifying the informed consent procedure to acknowledge that privacy cannot be guaranteed, and/or employing a secure cloud computing environment. Cloud computing in particular may allow access to the data in a more controlled fashion than the current practice of downloading and computing on large datasets. Furthermore, it may be particularly advantageous for small labs, given that the burden of many privacy issues falls disproportionately on them in comparison to large corporations and genome centers. Finally, we discuss how education of future genetics researchers will be important, with curriculums emphasizing privacy and data security. However, teaching personal genomics with identifiable subjects in the university setting will, in turn, create additional privacy issues and social conundrums.