Inferring protein-protein interacting sites using residue conservation and evolutionary information

This paper proposes a novel method using protein residue conservation and evolution information, i.e., spatial sequence profile, sequence information entropy and evolution rate, to infer protein binding sites. Some predictors based on support vector machines (SVMs) algorithm are constructed to predict the role of surface residues in protein-protein interface. By combining protein residue characters, the prediction performance can be improved obviously. We then made use of the predicted labels of neighbor residues to improve the performance of the predictors. The efficiency and the effectiveness of our proposed approach are verified by its better prediction performance based on a non-redundant data set of heterodimers.     

N-methyl-D-aspartate receptor subunits are non-myosin targets of myosin regulatory light chain

Excitatory synapses contain multiple members of the myosin superfamily of molecular motors for which functions have not been assigned. In this study we characterized the molecular determinants of myosin regulatory light chain (RLC) binding to two major subunits of the N-methyl-d-aspartate receptor (NR). Myosin RLC bound to NR subunits in a manner that could be distinguished from the interaction of RLC with the neck region of non-muscle myosin II-B (NMII-B) heavy chain; NR-RLC interactions did not require the addition of magnesium, were maintained in the absence of the fourth EF-hand domain of the light chain, and were sensitive to RLC phosphorylation. Equilibrium fluorescence spectroscopy experiments indicate that the affinity of myosin RLC for NR1 is high (30 nm) in the context of the isolated light chain. Binding was not favored in the context of a recombinant NMII-B subfragment one, indicating that if the RLC is already bound to NMII-B it is unlikely to form a bridge between two binding partners. We report that sequence similarity in the "GXXXR" portion of the incomplete IQ2 motif found in NMII heavy chain isoforms likely contributes to recognition of NR2A as a non-myosin target of the RLC. Using site-directed mutagenesis to disrupt NR2A-RLC binding in intact cells, we find that RLC interactions facilitate trafficking of NR1/NR2A receptors to the cell membrane. We suggest that myosin RLC can adopt target-dependent conformations and that a role for this light chain in protein trafficking may be independent of the myosin II complex.     

Traditional Chinese medicine Bak Foong Pills alters uterine quiescence – Possible role in alleviation of dysmenorrhoeal symptoms

Since contractility of the uterus appears to be the major source of pain during dysmenorrhoea, alleviation of the contractions is believed to be a possible treatment strategy. Bak Foong Pills, a traditional Chinese formulation for use in gynaecological disorders, has long been thought as effective in the treatment of dysmenorrhoeal symptoms. The present study thus aims to investigate whether ethanol extract of Bak Foong Pills (BFP-Ex) or its constituent herbs may have direct effects on alleviating dysmenorrhoeal symptoms by altering uterine tone. This was investigated using isolated uterine preparations and intracellular messenger analysis of adenylate cyclase, via [³H]-adenine assay, and calcium, with fluorometry imaging, in myometrial cultures. BFP-Ex can stimulate uterine relaxation following oxytocin-induced contractions ex-vivo. Attempted inhibition of BFP-Ex's relaxatory response with a nitric oxide inhibitor and adenylate cyclase inhibitor, however, had no significant effect, suggesting that most of BFP-Ex's relaxatory response was not due to increases in NO or cAMP. Further studies on tetramethylpyrazine (TMP), a major active ingredient of BFP-Ex, indicated that TMP could modulate intracellular calcium levels in favour of uteri relaxation. The ability of Bak Foong Pills to alleviate menstrual pain may be due to direct regulation of uterine tone.     

Soluble MICA and a MICA Variation as Possible Prognostic Biomarkers for HBV-Induced Hepatocellular Carcinoma

MHC class I polypeptide-related chain A (MICA) molecule is induced in response to viral infection and various types of stress. We recently reported that a single nucleotide polymorphism (SNP) rs2596542 located in the MICA promoter region was significantly associated with the risk for hepatitis C virus (HCV)-induced hepatocellular carcinoma (HCC) and also with serum levels of soluble MICA (sMICA). In this study, we focused on the possible involvement of MICA in liver carcinogenesis related to hepatitis B virus (HBV) infection and examined correlation between the MICA polymorphism and the serum sMICA levels in HBV-induced HCC patients. The genetic association analysis revealed a nominal association with an SNP rs2596542; a G allele was considered to increase the risk of HBV-induced HCC (P = 0.029 with odds ratio of 1.19). We also found a significant elevation of sMICA in HBV-induced HCC cases. Moreover, a G allele of SNP rs2596542 was significantly associated with increased sMICA levels (P = 0.009). Interestingly, HCC patients with the high serum level of sMICA (>5 pg/ml) exhibited poorer prognosis than those with the low serum level of sMICA (≤5 pg/ml) (P = 0.008). Thus, our results highlight the importance of MICA genetic variations and the significance of sMICA as a predictive biomarker for HBV-induced HCC.     

Cholesterol inhibits the insertion of the Alzheimer’s peptide Aβ(25–35) in lipid bilayers

The physiological relationship between brain cholesterol content and the action of amyloid β (Aβ) peptide in Alzheimer’s disease (AD) is a highly controversially discussed topic. Evidences for modulations of the Aβ/membrane interaction induced by plasma membrane cholesterol have already been observed. We have recently reported that Aβ(25–35) is capable of inserting in lipid membranes and perturbing their structure. Applying neutron diffraction and selective deuteration, we now demonstrate that cholesterol alters, at the molecular level, the capability of Aβ(25–35) to penetrate into the lipid bilayers; in particular, a molar weight content of 20% of cholesterol hinders the intercalation of monomeric Aβ(25–35) completely. At very low cholesterol content (about 1% molar weight) the location of the C-terminal part of Aβ(25–35) has been unequivocally established in the hydrocarbon region of the membrane, in agreement with our previous results on pure phospholipids membrane. These results link a structural property to a physiological and functional behavior and point to a therapeutical approach to prevent the AD by modulation of membrane properties.     

Seasonal patterns of birth in patients with glioblastoma

Seasonal distribution of birth rates was only recently described in patients with high-grade gliomas. We analyzed 501 cases from the database of a Regional Cancer Center in Bavaria to assess annual periodicity in the birth dates of glioma patients. Prior to analysis, the number of births per month was normalized [number of births×100,000/total number of births in Germany] to obtain birth rates per month. The approximation of the time series data by a one-year cosine model found that the glioblastoma birth rate exhibits a statistically significant annual variation, with the peak rate in January. Vitamin intake, infections, and other as-yet-unknown factors and exposures during pre- and perinatal early life may contribute to the seasonality of birth rate in patients with brain tumors.     

Novel Dielectric-Loaded Plasmonic Waveguide for Tight-Confined Hybrid Plasmon Mode

In this paper, a novel metal-dielectric waveguide structure is proposed to support hybrid long range surface plasmon polaritons (LRSPPs) with a highly confined mode field. The simulation results showed that our proposed structure has better mode confinement and propagation length compared to that of conventional dielectric-loaded surface plasmon polaritons (DLSPPs) waveguides. This structure offers greater flexibility for the design of surface plasmon polaritons (SPPs) waveguides by altering the trade-off between mode confinement and propagation length. The proposed structure has significant potential for application in highly integrated photonic circuits.     

Enemy at the Gates: Interaction-Specific Stomatal Responses to Pathogenic Challenge

Stomata regulate gas exchange and their closure in response to pathogens may, in some cases, contribute to resistance. However, in the cereal mildew and rust systems, stomatal closure follows establishment of compatible infections. In incompatible systems, expression of major (R) gene controlled hypersensitive responses (HR), causes drastic, permanent stomatal dysfunction: stomata become locked open following powdery mildew attack and locked shut following rust attack. Thus, stomatal locking can be a hitherto unsuspected negative consequence of R gene resistance that carries a physiological cost affecting plant performance.Key Words: stomata, rust, mildew, hypersensitive response, stomatal lock-up