A microstructurally informed model for the mechanical response of three-dimensional actin networks

We propose a class of microstructurally informed models for the linear elastic mechanical behaviour of cross-linked polymer networks such as the actin cytoskeleton. Salient features of the models include the possibility to represent anisotropic mechanical behaviour resulting from anisotropic filament distributions, and a power law scaling of the mechanical properties with the filament density. Mechanical models within the class are parameterized by seven different constants. We demonstrate a procedure for determining these constants using finite element models of three-dimensional actin networks. Actin filaments and cross-links were modelled as elastic rods, and the networks were constructed at physiological volume fractions and at the scale of an image voxel. We show the performance of the model in estimating the mechanical behaviour of the networks over a wide range of filament densities and degrees of anisotropy.     

Isolation and characterization of a mycovirus in Lentinula edodes

A mycovirus was isolated from an edible mushroom, Lentinula edodes, that was suffering from a severe epidemic. Fractionation of the diseased cell extract by isopycnic centrifugation with 50% CsCl revealed that the diseased mushroom was infected by Lentinula edodes spherical virus (LeSV), a new spherical virus with a diameter of 55 nm. The particle of LeSV encapsidated the 12 kb RNA genome by a 120 kDa coat protein. BLAST analysis of the partially sequenced LeSV genome showed 95% sequence identity with a putative RNA-dependent RNA polymerase (RdRp) gene of the mycovirus HKB, which was previously reported as being a double-stranded RNA (dsRNA) element. In contrast to HKB, the RNA genome in LeSV is encapsidated by the 120 kDa coat protein. To confirm that the LeSV coat protein is encoded by the viral genome, the N-terminal amino acid sequence of the coat protein was determined. The resulting N-terminal amino acid sequence, N-SALDVAPVVPELYFXXLEV-C, was found to be located in the middle of the HKB ORF1, suggesting that the LeSV coat protein was indeed encoded by the virus. To detect LeSV in L. edodes, a primer set targeting the RdRp gene was designed based on the partial sequence of the LeSV genome. RT-PCR analysis showed that 56 of the 84 commercially available dikaryotic cultivars carry LeSV. The transmission pattern of the virus was determined by analysing basidiospores from LeSV-infected and LeSV-free fruiting bodies. Nine out of 10 basidiospores from the LeSV-infected cultivars contained the virus while the spores from the LeSV-free parent were free of LeSV, suggesting that vertical transmission is the primary mode of LeSV propagation.     

Rhodanobacter umsongensis sp. nov., isolated from a Korean ginseng field

A bacterial isolate designated GR24-2^T was isolated from Korean soil used for cultivating ginseng (Panax ginseng C. A. Meyer). The strain was aerobic, Gram-negative, motile, and rod-shaped. It grew optimally at 28–30°C, pH 7.0, and in a range of 0–1% NaCl. Phylogenetically, the strain clustered with members of the genus Rhodanobacter. The strain exhibited the highest sequence similarities (>98%) with R. panaciterrae LnR5-47^T (98.4%), R. soli DCY45^T (98.2%), and R. ginsengisoli GR17-7^T (98.0%). However, it also showed high sequence similarities (>97%) with some other Rhodanobacter and Dyella species. The strain contained Q-8 as the predominant respiratory quinone. The major fatty acids (greater than 10% of the total fatty acids) were iso-C_17:1 ω9c (24.5%), iso-C_16:0 (22.8%), anteiso-C_15:0 (10.5%), and iso-C_15:0 (10.1%). Its major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unknown aminophospholipid. The DNA G+C content of strain GR24-2^T was 65.6 mol%. The strain showed less than 70% DNA relatedness values between the closely related Rhodanobacter and Dyella species. The phylogeny, phenotype, DNA-DNA hybridization, and chemotaxonomic data generated in this study reveal that the isolate is a novel species of the genus Rhodanobacter. The name proposed for this strain is Rhodanobacter umsongensis sp. nov. (type strain GR24-2^T =KACC 12917^T =DSM 21300^T).     

Sublingual administration of bacteria-expressed influenza virus hemagglutinin 1 (HA1) induces protection against infection with 2009 pandemic H1N1 influenza virus

Influenza viruses are respiratory pathogens that continue to pose a significantly high risk of morbidity and mortality of humans worldwide. Vaccination is one of the most effective strategies for minimizing damages by influenza outbreaks. In addition, rapid development and production of efficient vaccine with convenient administration is required in case of influenza pandemic. In this study, we generated recombinant influenza virus hemagglutinin protein 1 (sHA1) of 2009 pandemic influenza virus as a vaccine candidate using a well-established bacterial expression system and administered it into mice via sublingual (s.l.) route. We found that s.l. immunization with the recombinant sHA1 plus cholera toxin (CT) induced mucosal antibodies as well as systemic antibodies including neutralizing Abs and provided complete protection against infection with pandemic influenza virus A/CA/04/09 (H1N1) in mice. Indeed, the protection efficacy was comparable with that induced by intramuscular (i.m.) immunization route utilized as general administration route of influenza vaccine. These results suggest that s.l. vaccination with the recombinant non-glycosylated HA1 protein offers an alternative strategy to control influenza outbreaks including pandemics.     

Pontibacter jeungdoensis sp. nov., isolated from a solar saltern in Korea

A Gram-staining-negative, rod-shaped and red-pigmented bacterial strain, HMD3125^T, was isolated from a solar saltern in Jeungdo, Republic of Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD3125^T formed a lineage within the genus Pontibacter and was similar to Pontibacter salisaro (96.1%) and P. korlensis (95.3%). The major fatty acids of strain HMD3125^T were summed feature 4 (comprising iso-C_17:1 I and/or anteiso-C_17:1 B; 30.4%), iso-C_15:0 (20.4%) and iso-C_17:0 3OH (17.2%). The polar lipid profile of HMD3125^T consisted of the phosphatidylethanolamine, four unidentified polar lipids, unidentified phospholipid, unidentified aminolipid and unidentified aminophospholipid. Strain HMD3125^T contained MK-7 as the predominant menaquinone and sym-homospermidine as the major polyamine. The DNA G+C content of strain HMD3125^T was 45.6 mol%. Strain HMD3125^T assigned as a novel species in the genus Pontibacter, for which the name Pontibacter jeungdoensis sp. nov. is proposed. The type strain is HMD3125^T (=KCTC 23156^T =CECT 7710^T).     

M-Finder: Uncovering functionally associated proteins from interactome data integrated with GO annotations

Background

Protein-protein interactions (PPIs) play a key role in understanding the mechanisms of cellular processes. The availability of interactome data has catalyzed the development of computational approaches to elucidate functional behaviors of proteins on a system level. Gene Ontology (GO) and its annotations are a significant resource for functional characterization of proteins. Because of wide coverage, GO data have often been adopted as a benchmark for protein function prediction on the genomic scale.

Results

We propose a computational approach, called M-Finder, for functional association pattern mining. This method employs semantic analytics to integrate the genome-wide PPIs with GO data. We also introduce an interactive web application tool that visualizes a functional association network linked to a protein specified by a user. The proposed approach comprises two major components. First, the PPIs that have been generated by high-throughput methods are weighted in terms of their functional consistency using GO and its annotations. We assess two advanced semantic similarity metrics which quantify the functional association level of each interacting protein pair. We demonstrate that these measures outperform the other existing methods by evaluating their agreement to other biological features, such as sequence similarity, the presence of common Pfam domains, and core PPIs. Second, the information flow-based algorithm is employed to discover a set of proteins functionally associated with the protein in a query and their links efficiently. This algorithm reconstructs a functional association network of the query protein. The output network size can be flexibly determined by parameters.

Conclusions

M-Finder provides a useful framework to investigate functional association patterns with any protein. This software will also allow users to perform further systematic analysis of a set of proteins for any specific function. It is available online at http://bionet.ecs.baylor.edu/mfinder

     

Overexpression of Neurospora crassa OR74A glutamate decarboxylase in Escherichia coli for efficient GABA production

This study investigated the effect of glutamate decarboxylase from Neurospora crassa OR74A on GABA production in Escherichia coli. GABA is one of the inhibitory neurotransmitters in the mammalian central nervous system, and can be used as a precursor of promising biopolymer Nylon 4. E. coli that overexpressed N. crassa glutamate decarboxylase was cultured at various pH levels and temperatures to determine optimum conditions for GABA production. When the recombinant E. coli strain was cultured at 30°C and pH 3, a final GABA concentration of 5.26 g/L was obtained from 10 g/L of monosodium glutamate (MSG), corresponding to a GABA yield of 86.23%.