A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions

Halogen bonding, a non-covalent interaction between the halogen σ-hole and Lewis bases, could not be properly characterized by majority of current scoring functions. In this study, a knowledge-based halogen bonding scoring function, termed XBPMF, was developed by an iterative method for predicting protein-ligand interactions. Three sets of pairwise potentials were derived from two training sets of protein-ligand complexes from the Protein Data Bank. It was found that two-dimensional pairwise potentials could characterize appropriately the distance and angle profiles of halogen bonding, which is superior to one-dimensional pairwise potentials. With comparison to six widely used scoring functions, XBPMF was evaluated to have moderate power for predicting protein-ligand interactions in terms of “docking power”, “ranking power” and “scoring power”. Especially, it has a rather satisfactory performance for the systems with typical halogen bonds. To the best of our knowledge, XBPMF is the first halogen bonding scoring function that is not dependent on any dummy atom, and is practical for high-throughput virtual screening. Therefore, this scoring function should be useful for the study and application of halogen bonding interactions like molecular docking and lead optimization.

Study on the Interaction Mechanism of 2‐Aminoanthraquinone with Calf Thymus DNA

By utilizing multispectrosopic techniques, the toxic interaction of 2‐aminoanthraquinone (2‐AAQ) with calf thymus deoxyribonucleic acid (ctDNA) was investigated in vitro under simulated physiological conditions. The experimental results proved that 2‐AAQ has a toxic interaction with ctDNA. The binding capacity of DNA with 2‐AAQ is diminishing as the pH value of system increasing in the optimization of experimental condition. Moreover we selected pH 7.4, which is nearly physiological condition to enhance the practical significance. According to the Stern–Volmer equation, the quenching was the static quenching process. And the quenching constant can be derived from the fluorescence quenching spectrogram. Ultraviolet absorption spectra and the change in the fluorescence intensity at different ionic strengths further indicated that there was electrostatic binding between 2‐AAQ and ctDNA. The circular dichroism experiment showed that the DNA conformation varied from B to A conformation. The basic group enhanced after 2‐AAQ embedding. The double helix is more compact, and the DNA conformation changes. © 2013 Wiley Periodicals, Inc. J BiochemMol Toxicol 27:272‐278, 2013; View this article online at wileyonlinelibrary.com . DOI 10.1002/jbt.21487     

Recovery of native protein from potato root water by expanded bed adsorption with amberlite XAD7HP

Potato root water (PRW) contains ～1.5% protein. In this study, expanded bed adsorption (EBA) chromatography with Amberlite XAD7HP resin adsorbent was used to isolate native protein from crude PRW. The optimal pH and ionic strength for potato protein binding onto Amberlite XAD7HP were 5.0 and 20 mmol/L. The EBA-refined proteins were dried by vacuum freeze drying and spray drying at varying outlet temperatures. Results indicated that low temperature spray drying was the most cost effective method with respect to retaining protease inhibitor activities. The dried protein concentrates appeared bright yellow or dark reddish brown, with a total glycoalkaloid content of ～170 μg/g. The protease inhibitor activity was ～400 mg/g and 11 ～ 12 mg/g for trypsin inhibition and chymotrypsin inhibition, respectively. The results presented here suggest that EBA using Amberlite XAD7HP as the adsorbent is a feasible strategy for the direct adsorption of native protein from crude PRW.     

Pushing short DNA fragments to the limit: Phylogenetic relationships of ‘hydrobioid’ gastropods (Caenogastropoda: Rissooidea)

Although phylogenetic studies are increasingly utilizing multi-locus datasets, a review of GenBank data for the Gastropoda indicates a strong bias towards a few short gene fragments (most commonly COI, LSU rRNA, and SSU rRNA). This is particularly the case for the Rissooidea, one of the largest and most taxonomically difficult gastropod superfamilies. Here we analyze fragments of these three genes from 90 species to determine whether they can well resolve higher relationships within this superfamily, whether structurally aligned sequence datasets increase phylogenetic signal, and whether the inclusion of highly variable regions introduces noise. We also used the resulting phylogenetic data in combination with morphological/anatomical evidence to re-evaluate the taxonomic status of ‘hydrobioid’ family-level groups.Our results indicate that all three of the alignment strategies that were used resulted in phylogenies having similar signal levels. However, there was a slight advantage to using structural alignment for inferring family-level relationships. Moreover, the set of ‘standard’ gastropod genes supported recognition of many previously recognized families and provides new insight into the systematics of several problematic groups. However, some family-group taxa were unresolved and the relationships among families were also poorly supported, suggesting a need for more extensive sampling and inclusion of additional genes.     

Opinion survey of the Hong Kong general public regarding genomic science and technology and their ethical and social implications

The study's objective is to survey the attitudes of Chinese people living in Hong Kong toward genomic science and technology (GST) and their ethical and social implications. Using a 24-item questionnaire, 877 Cantonese-speaking residents between age 18 and 64 with minimum high school education are interviewed by telephone. Multiple regression analysis identifies education level as the most important demographic variable. Overall, respondents have mild agreement with genetic determinism and the use of GST for disease prevention but not for non-therapeutic genetic enhancement and production of “genetically modified” crops or meat. Respondents strongly believe that GST tampers with nature and resources should be used to solve other healthcare problems first. Respondents also show little concern that personal genetic information may be abused by their employers or schools and have only a minimal willingness to share personal genetic information with their family members.     

Ve1‐mediated resistance against Verticillium does not involve a hypersensitive response in Arabidopsis

The recognition of pathogen effectors by plant immune receptors leads to the activation of immune responses that often include a hypersensitive response (HR): rapid and localized host cell death surrounding the site of attempted pathogen ingress. We have demonstrated previously that the recognition of the Verticillium dahliae effector protein Ave1 by the tomato immune receptor Ve1 triggers an HR in tomato and tobacco. Furthermore, we have demonstrated that tomato Ve1 provides Verticillium resistance in Arabidopsis upon Ave1 recognition. In this study, we investigated whether the co‐expression of Ve1 and Ave1 in Arabidopsis results in an HR, which could facilitate a forward genetics screen. Surprisingly, we found that the co‐expression of Ve1 and Ave1 does not induce an HR in Arabidopsis. These results suggest that an HR may occur as a consequence of Ve1/Ave1‐induced immune signalling in tomato and tobacco, but is not absolutely required for Verticillium resistance.     

Optimizing dopaminergic differentiation of pluripotent stem cells for the manufacture of dopaminergic neurons for transplantation

Background aimsWe have previously described a xeno-free scalable system to generate transplantable dopaminergic neurons from human pluripotent stem cells. However, several important questions remain to be answered about our cell therapy efforts. These include determining the exact time at which cells should be transplanted and whether cells at this stage can be frozen, shipped, thawed and injected without compromising their ability to mature and survive the transplantation procedure. We also needed to determine whether further optimization of the culture process could shorten the development time and reduce variability and whether a current Good Manufacture Practice (CGMP) facility could manufacture cells with fidelity.MethodsWe developed an optimized protocol that included modulating the sonic hedgehog homolog gradient with bone morphogenetic proteins (BMP2) and addition of activin to the culture medium, which shortened the time to generate Lmx1A and FoxA2 immunoreactive cells by 4–6 days.ResultsWe showed that cells at this stage could be safely frozen and thawed while retaining an excellent ability to continue to mature in vitro and survive transplant in vivo. Importantly, we successfully adapted this process to a CGMP facility and manufactured two lots of transplant-ready dopaminergic neurons (>250 vials) under CGMP-compatible conditions. In vitro characterization, including viability/recovery on thawing, whole genome expression as well as expression of midbrain/dopaminergic markers, showed that the cells manufactured under GMP-compatible conditions were similar to cells produced at lab scale.ConclusionsOur results suggest that this optimized protocol can be used to generate dopaminergic neurons for Investigational New Drug enabling studies.     

Involvement of FgERG4 in ergosterol biosynthesis,vegetative differentiation and virulence in Fusarium graminearum

The ergosterol biosynthesis pathway is well understood in Saccharomyces cerevisiae, but currently little is known about the pathway in plant‐pathogenic fungi. In this study, we characterized the Fusarium graminearum FgERG4 gene encoding sterol C‐24 reductase, which catalyses the conversion of ergosta‐5,7,22,24‐tetraenol to ergosterol in the final step of ergosterol biosynthesis. The FgERG4 deletion mutant ΔFgErg4‐2 failed to synthesize ergosterol. The mutant exhibited a significant decrease in mycelial growth and conidiation, and produced abnormal conidia. In addition, the mutant showed increased sensitivity to metal cations and to various cell stresses. Surprisingly, mycelia of ΔFgErg4‐2 revealed increased resistance to cell wall‐degrading enzymes. Fungicide sensitivity tests revealed that ΔFgErg4‐2 showed increased resistance to various sterol biosynthesis inhibitors (SBIs), which is consistent with the over‐expression of SBI target genes in the mutant. ΔFgErg4‐2 was impaired dramatically in virulence, although it was able to successfully colonize flowering wheat head and tomato, which is in agreement with the observation that the mutant produces a significantly lower level of trichothecene mycotoxins than does the wild‐type progenitor. All of these phenotypic defects of ΔFgErg4‐2 were complemented by the reintroduction of a full‐length FgERG4 gene. In addition, FgERG4 partially rescued the defect of ergosterol biosynthesis in the Saccharomyces cerevisiae ERG4 deletion mutant. Taken together, the results of this study indicate that FgERG4 plays a crucial role in ergosterol biosynthesis, vegetative differentiation and virulence in the filamentous fungus F. graminearum.