Interspecific interactions among species of the coral genus Porites from Okinawa, Japan

Analysis of field established xenogeneic interactions among five Porites species from Sesoko Island, Okinawa, revealed a transitive type of hierarchy as: P. rus > P. cylindrica > P. lobata > P. australiensis> P. lutea. Out of the 111 interspecific encounters studied, in only 5.4% reciprocal interactions were recorded, and in a single case, the opposite directionality of hierarchy was documented. Allogeneic encounters were also observed. A single major effector mechanism, an overgrowth (together with secondary outcomes such as the formation of small points of rejection, bleaching and pink color formation along a narrow peripheral belt of contacting tissues), was the only response in all 10 xenogeneic and 5 allogeneic combinations. In some massive colonies, a long contacting line of up to 50 cm was established. No sign for allelopathy, stand-off or rejection from a distance (i.e., by sweeper tentacles, sweeper polyps) was observed. Results are discussed with the accumulated data on Porites species from different reefs, worldwide, confirming that this genus is commonly lower in the hierarchy of xenogeneic interactions.     

Improved protein-ligand docking using GOLD

The Chemscore function was implemented as a scoring function for the protein-ligand docking program GOLD, and its performance compared to the original Goldscore function and two consensus docking protocols, "Goldscore-CS" and "Chemscore-GS," in terms of docking accuracy, prediction of binding affinities, and speed. In the "Goldscore-CS" protocol, dockings produced with the Goldscore function are scored and ranked with the Chemscore function; in the "Chemscore-GS" protocol, dockings produced with the Chemscore function are scored and ranked with the Goldscore function. Comparisons were made for a "clean" set of 224 protein-ligand complexes, and for two subsets of this set, one for which the ligands are "drug-like," the other for which they are "fragment-like." For "drug-like" and "fragment-like" ligands, the docking accuracies obtained with Chemscore and Goldscore functions are similar. For larger ligands, Goldscore gives superior results. Docking with the Chemscore function is up to three times faster than docking with the Goldscore function. Both combined docking protocols give significant improvements in docking accuracy over the use of the Goldscore or Chemscore function alone. "Goldscore-CS" gives success rates of up to 81% (top-ranked GOLD solution within 2.0 A of the experimental binding mode) for the "clean list," but at the cost of long search times. For most virtual screening applications, "Chemscore-GS" seems optimal; search settings that give docking speeds of around 0.25-1.3 min/compound have success rates of about 78% for "drug-like" compounds and 85% for "fragment-like" compounds. In terms of producing binding energy estimates, the Goldscore function appears to perform better than the Chemscore function and the two consensus protocols, particularly for faster search settings. Even at docking speeds of around 1-2 min/compound, the Goldscore function predicts binding energies with a standard deviation of approximately 10.5 kJ/mol.     

On the accuracy of analytical potentials: comment on ‘Accurate ab initio calculation of the Ar–CF4 intermolecular potential energy surface’

In a recent study of the Ar–CF₄ intermolecular interaction potential [Shen C-C, Chang R-Y. Accurate ab initio calculation of the Ar–CF₄ intermolecular potential energy surface. Mol Sim. 2010;36:1111–1122], Shen and Chang (SC) illustrated how the use of bond functions can improve the accuracy and basis-set saturation of electronic structure calculations employing perturbation and coupled-cluster theory. SC then used these ab initio data to derive analytic potential energy functions for use in chemical dynamics simulations. We critically examine these analytic potentials and comment on their usage in such simulations. Our analysis highlights the need for care and global validation when deriving analytic potential energy functions.     

New weapons in the war on worms: identification of putative mechanisms of immune-mediated expulsion of gastrointestinal nematodes

Parasitic nematode infections of humans and livestock continue to impose a significant public health and economic burden worldwide. Murine models of intestinal nematode infection have proved to be relevant and tractable systems to define the cellular and molecular basis of how the host immune system regulates resistance and susceptibility to infection. While susceptibility to chronic infection is propagated by T helper cell type 1 cytokine responses (characterised by production of IL-12, IL-18 and interferon-gamma), immunity to intestinal-dwelling adult nematode worms is critically dependent on a type 2 cytokine response (controlled by CD4+T helper type 2 cells that secrete the cytokines IL-4, IL-5, IL-9 and IL-13). However, the immune effector mechanisms elicited by type 2 cytokines in the gut microenvironment that precipitate worm expulsion have remained elusive. This review focuses on new studies that implicate host intestinal epithelial cells as one of the dominant immune effector cells against this group of pathogens. Specifically, three recently identified type 2 cytokine-dependent pathways that could offer insights into the mechanisms of expulsion of parasitic nematodes will be discussed: (i) the intelectins, a new family of galactose-binding lectins implicated in innate immunity, (ii) the resistin-like molecules, a family of small cysteine-rich proteins expressed by multiple cell types, and (iii) cytokine regulation of intestinal epithelial cell turnover. Identifying how the mammalian immune response fights gastrointestinal nematode infections is providing new insights into host protective immunity. Harnessing these discoveries, coupled with identifying what the targets of these responses are within parasitic nematodes, offers promise in the design of a new generation of anti-parasitic drugs and vaccines.     

Pyromeconic Acid and Its Glucosidic Derivatives from Leaves of Erigeron annuus,and the Siderophile Activity of Pyromeconic Acid

3′-O-Caffeylerigeroside (pyromeconic acid 3-O-β-D-glucoside 3′-O-caffeyl ester) was obtained from the leaves of Erigeron annuus as a new pyromeconic acid derivative, and its structure was elucidated. Together with the γ-pyrone derivative, pyromeconic acid (3-hydroxy-4H-pyran-4-one) and its β-glucoside (erigeroside) were also isolated from the aerial parts of E. annuus. The siderophile activity of pyromeconic acid was also studied.     

Efficient Detection, Quantification and Enrichment of Subtle Allelic Alterations

Gene targeting (GT) can introduce subtle alterations into a particular locus and represents a powerful tool for genome editing. Engineered zinc finger nucleases (ZFNs) are effective for generating minor allelic alterations. Efficient detection of such minor alterations remains one of the challenges in ZFN-mediated GT experiments. Here, we report the establishment of procedures allowing for efficient detection, quantification and enrichment of such subtle alterations. In a biallelic model, polyacrylamide gel electrophoresis (PAGE) is capable of detecting rare allelic variations in the form of DNA heteroduplexes at a high efficiency of ∼0.4% compared with ∼6.3% by the traditional T7 endonuclease I-digestion and agarose gel electrophoresis. In a multiple allelic model, PAGE could discriminate different alleles bearing addition or deletion of 1–18 bp as distinct bands that were easily quantifiable by densitometry. Furthermore, PAGE enables enrichment for rare alleles. We show for the first time that direct endogenous GT is possible in medaka by ZFN RNA injection, whereas PAGE allows for detection and cloning of ZFN-targeted alleles in adults arising from ZFN-injected medaka embryos. Therefore, PAGE is effective for detection, quantification and enrichment of multiple fine allelic differences and thus offers a versatile tool for screening targeted subtle gene alterations.