Protein secondary structure prediction using NMR chemical shift data

Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b) easily extendable to (the dynamic) new databases; and (c) approaching to the limit of accuracy. We introduce new approaches using k-nearest neighbor algorithm to do the basic prediction and use the BCJR algorithm to smooth the predictions and combine different predictions from chemical shifts and based on sequence information only. Our new system, SUCCES, improves the accuracy of all existing methods on a large dataset of 805 proteins (at 86% Q(3) accuracy and at 92.6% accuracy when the boundary residues are ignored), and it is easily extendable to any new dataset without requiring any new training. The software is publicly available at http://monod.uwaterloo.ca/nmr/succes.     

The dynamic nature of contact networks in infectious disease epidemiology

Although contact network models have yielded important insights into infectious disease transmission and control throughout the last decade, researchers have just begun to explore the dynamic nature of contact patterns and their epidemiological significance. Most network models have assumed that contacts are static through time. Developing more realistic models of the social interactions that underlie the spread of infectious diseases thus remains an important challenge for both data gatherers and modelers. In this article, we review some recent data-driven and process-driven approaches that capture the dynamics of human contact, and discuss future challenges for the field.     

Features analysis for identification of date and party hubs in protein interaction network of <Emphasis Type="Italic">Saccharomyces Cerevisiae</Emphasis>

Background  

It has been understood that biological networks have modular organizations which are the sources of their observed complexity. Analysis of networks and motifs has shown that two types of hubs, party hubs and date hubs, are responsible for this complexity. Party hubs are local coordinators because of their high co-expressions with their partners, whereas date hubs display low co-expressions and are assumed as global connectors. However there is no mutual agreement on these concepts in related literature with different studies reporting their results on different data sets. We investigated whether there is a relation between the biological features of Saccharomyces Cerevisiae 's proteins and their roles as non-hubs, intermediately connected, party hubs, and date hubs. We propose a classifier that separates these four classes.     

Structure and function: heat shock proteins and adaptive immunity

Heat shock proteins (HSPs) have been implicated in the stimulation and generation of both innate and adaptive immunity. The ability of HSPs to bind antigenic peptides and deliver them to APCs is the basis of the generation of peptide-specific T lymphocyte responses both in vitro and in vivo. The different HSP families are genetically and biochemically unrelated, and the structural basis of peptide binding and the dynamic models of ligand interaction are known only for some of the HSPs. We examine the contribution of HSP structure to its immunological functions and the potential "immunological repertoire" of HSPs as well as the use of biophysical techniques to quantify HSP-peptide interactions and optimize vaccine design. Although biochemical evidence for HSP-mediated endogenous processing of Ag has now emerged, the issue of whether HSP-peptide complexes act as physiological sources of Ag in cross-presentation is controversial. We assess the contribution of biochemical studies in this field.     

Modification of the Stewart biphasic colorimetric assay for stable and accurate quantitative determination of Pluronic and Tetronic block copolymers for application in biological systems

Block copolymers are increasingly being applied in areas such as transfection, membrane sealing, site-specific targeting, and bionanoengineering yet there is a relative paucity of assays available for simple, stable and reproducible colorimetric determination of copolymer concentration in solution. We have focused on improving the accuracy and reproducibility of a modified version of the Stewart biphasic colorimetric assay for quantitative determination of Pluronic (poloxamer) and Tetronic (poloxamine) macromolecules. The optimized assay achieved linear response ranges in chloroform for commonly used copolymers such as poloxamine 904 (20-300 microg/ml), poloxamine 908 (10-400 microg/ml), poloxamer 402 (20-400 microg/ml), and poloxamer 407 (10-400 microg/ml). Variation in the type of chlorinated solvent used significantly increased assay sensitivity, presumably through macromolecular reorientation, affording increased access for copolymer-ferrothiocyanate complexation. This was found to be optimally favored by the planar geometry of the solvent cis 1,2-dichloroethylene. For application to biological systems copolymer-protein interactions were for the first time determined and were found to be dependent on the fraction of hydrophobic constituents of the block copolymers and protein type. For instance serum albumin was found to interact with copolymers of low hydrophilic-lipophilic balance values and poly(propylene oxide) contaminants, whereas this interaction was not significant with the relatively hydrophilic IgG. In such systems the colorimetric assay directly determines the fraction of unbound (free) copolymer in the presence of proteins.     

Induction of Hsp22 (HspB8) by estrogen and the metalloestrogen cadmium in estrogen receptor-positive breast cancer cells

Estrogen (E2) plays a critical role in the etiology and progression of human breast cancer. The estrogenic response is complex and not completely understood, including in terms of the involved responsive genes. Here we show that Hsp22 (synonyms: HspB8, E2lG1, H11), a member of the small heat shock protein (sHSP) superfamily, was induced by E2 in estrogen receptor-positive MCF-7 breast cancer cells, resulting in an elevated Hsp22 protein level, whereas it was not induced in estrogen receptor-negative MDA-MB-231 cells. This induction was prevented by the pure anti-estrogen ICI182780 (faslodex, fulvestrant), whereas tamoxifen, a substance with mixed estrogenic and antiestrogenic properties, had no major inhibitory effect on this induction, nor did it induce Hsp22 on its own. Cadmium (Cd) is an environmental pollutant with estrogenic properties (metalloestrogen) that has been implicated in breast cancer. Treatment of MCF-7 cells with Cd also resulted in induction of Hsp22, and this induction was also inhibited by ICI182780. In live MCF-7 cells, Hsp22 interacted at the level of dimers with Hsp27, a related sHSP, as was shown by quantitative fluorescence resonance energy transfer measurements. In cytosolic extracts of MCF-7 cells, most of the E2- and Cd-induced Hsp22 was incorporated into high-molecular mass complexes. In part, Hsp22 and Hsp27 were components of distinct populations of these complexes. Finally, candidate elements in the Hsp22 promoter were identified by sequence analysis that could account for the induction of Hsp22 by E2 and Cd. Taken together, Hsp22 induction represents a new aspect of the estrogenic response with potential significance for the biology of estrogen receptor-positive breast cancer cells.     

First Report of Curtobacterium flaccumfaciens pv. flaccumfaciens Causing Cowpea Bacterial Wilt in Iran

During surveys in cowpea fields of Marand County, East Azerbaijan province, Iran, in the summer of 2013, a suspected bacterial disease was observed on cowpea leaves as tan spots and interveinal necrotic lesions surrounded by chlorotic margins. The disease was of high incidence where some fields had been fully destroyed and severity of the disease in some fields had reached up to 70%. Gram‐positive, yellow‐pigmented, coryneform bacteria were isolated from infected leaves. Pathogenicity of isolates was confirmed on 20‐day‐old cowpea (cv. Khoy) plants, and they were identified as Curtobacterium flaccumfaciens pv. flaccumfaciens based on biochemical test results confirmed using specific PCR primers. This is the first report of C. flaccumfaciens pv. flaccumfaciens, the causal agent of cowpea bacterial wilt in Iran.