From subgenome analysis to protein structure

Groups of related genes abound in large eukaryotic genomes. In such 'subgenomes', homology modeling carried out for a few genes will probably have relevance to the entire group. Subgenomes also afford unique ways of determining protein structural information. In addition to analyses based on the quantification of residue variability in paralogs, two-way comparisons, both within and among species, help to disclose functional amino acids. Comparative studies of gene families throughout the mammalian genome will also help elucidate the functional significance of single nucleotide polymorphisms in coding regions.     

Crystal structures of two homologous pathogenesis-related proteins from yellow lupine

Pathogenesis-related class 10 (PR10) proteins are restricted to the plant kingdom where they are coded by multigene families and occur at high levels. In spite of their abundance, their physiological role is obscure although members of a distantly related subclass (cytokinin-specific binding proteins) are known to bind plant hormones. PR10 proteins are of special significance in legume plants where their expression patterns are related to infection by the symbiotic, nitrogen-fixing bacteria. Here we present the first crystal structures of classic PR10 proteins representing two homologues from one subclass in yellow lupine. The general fold is similar and, as in a birch pollen allergen, consists of a seven-stranded beta-sheet wrapped around a long C-terminal helix. The mouth of a large pocket formed between the beta-sheet and the helix seems a likely site for ligand binding. The shape of the pocket varies because, in variance with the rigid beta-sheet, the helix shows unusual conformational variability consisting in bending, disorder, and axial shifting. A surface loop, proximal to the entrance to the internal cavity, shows an unusual structural conservation and rigidity in contrast to the high glycine content in its sequence. The loop is different from the so-called glycine-rich P-loops that bind phosphate groups of nucleotides, but it is very likely that it does play a role in ligand binding in PR10 proteins.     

Effects of nonwoven mats of Di-O-butyrylchitin and related polymers on the process of wound healing

The aim of the study was to observe the effects of dibutyrylchitin (DBC) on the repair processes and to explain the mechanisms of its action in comparison with other dressing materials made of butyrylchitin (BC), regenerated chitin (RC), and chitosan. The results showed that DBC implanted subcutaneously to the rats increased weight of the granulation tissue. Increased cell number isolated from the wound and cultured on the DBC films was also revealed. The DBC was proved to reduce also the necrotic cells number in the culture. DBC elevates the glycosaminoglycans (GAG) level in the granulation tissue. The total collagen content in the wound was not influenced by all applied dressing materials. However, a low level of the poorly polymerized soluble collagen in the wounds treated with DBC and BC indicated better polymerization of the remaining part of that protein. Both DBC and chitosan increased the weight of granulation tissue. However, chitosan contrary to DBC lowered GAG content and increased water capacity in the wound. The study documents the beneficial influence of DBC on the repair, which could be explained by the modification of the extracellular matrix and cells number. The best effects were observed after application of DBC with [eta] DBC-1 = 1.75 dL/g.     

Gene Expression Signature Differentiates Histology But Not Progression Status of Early-Stage NSCLC

Advances in molecular analyses based on high-throughput technologies can contribute to a more accurate classification of non–small cell lung cancer (NSCLC), as well as a better prediction of both the disease course and the efficacy of targeted therapies. Here we set out to analyze whether global gene expression profiling performed in a group of early-stage NSCLC patients can contribute to classifying tumor subtypes and predicting the disease prognosis. Gene expression profiling was performed with the use of the microarray technology in a training set of 108 NSCLC samples. Subsequently, the recorded findings were validated further in an independent cohort of 44 samples. We demonstrated that the specific gene patterns differed significantly between lung adenocarcinoma (AC) and squamous cell lung carcinoma (SCC) samples. Furthermore, we developed and validated a novel 53-gene signature distinguishing SCC from AC with 93% accuracy. Evaluation of the classifier performance in the validation set showed that our predictor classified the AC patients with 100% sensitivity and 88% specificity. We revealed that gene expression patterns observed in the early stages of NSCLC may help elucidate the histological distinctions of tumors through identification of different gene-mediated biological processes involved in the pathogenesis of histologically distinct tumors. However, we showed here that the gene expression profiles did not provide additional value in predicting the progression status of the early-stage NSCLC. Nevertheless, the gene expression signature analysis enabled us to perform a reliable subclassification of NSCLC tumors, and it can therefore become a useful diagnostic tool for a more accurate selection of patients for targeted therapies.     

A Human Health Risk Assessment Software for Facilitating Management of Urban Contaminated Sites: A Case Study: The Massa Site,Tuscany, Italy

The goal of this article is to present the Human Health Risk Assessment (HRA) software developed as one of the NORISC ^{1 1}NORISC is the acronym of the project “Network Oriented Risk assessment by In-situ Screening of Contaminated sites” realized under under the 5th European Union Community Framework Programme for Research, Technological Development and Demonstration Activities. View all notes decision support software system components that could be used as a tool for facilitating management of urban contaminated sites. The NORISC-HRA software provides sufficient technical and procedural support to conduct a simple site-specific risk assessment. The employed HRA methodology is generally based on U.S. Environmental Protection Agency (USEPA) procedures. The software determines the level and spatial distribution of human health risks at a given site and sets up site-specific preliminary Health-Based Remedial Goals (HBRGs)/Risk-Based Concentrations (RBCs) for soil and groundwater. The NORISC-HRA software is recommended for use when national soil and groundwater limit values are exceeded. Exposure pathways considered in this software are associated with three land use patterns—residential, industrial/commercial, and recreational. The aricle also presents the software testing results obtained at one of the NORISC test sites—the Massa site (Avenza-Carrara, Tuscany, Italy). Findings of the HRA indicated that the contaminated soil at the Massa test site might pose potential cancer and non-cancer risks to industrial workers in its present condition. Arsenic was the dominant substance responsible for most of the baseline risk and at the RBC of 1.77 mg/kg it was the primary driver of remedial decisions at the Massa site.     

Enhanced production of the pharmaceutically important polyphenolic compounds in Vitex agnus castus L. shoot cultures by precursor feeding strategy

Agitated Vitex agnus castus L. shoot cultures were established to analyse the content of selected pharmaceutically important flavonoids and phenolic acids. Two variants (selected from nine ones) of MS medium were prepared: A (BAP 1 mg/L; NAA 0.5 mg/L; GA₃ 0.25 mg/L) and B (BAP 2 mg/L; NAA 0.5 mg/L). The biomass was harvested after 1, 2, 3,4, 5 and 6 weeks. Four‐week cultures (variant A) were selected to perform the precursor feeding experiment. The L‐phenylalanine dose of 1.6 g/L appears to be the most advantageous. Compared to the control cultures, the content of the individual compounds increased in a range from 1.4 to 17.3‐fold (e.g. p‐coumaric acid – 17.3 fold; casticin – 4.8‐fold). The biomass from in vitro cultures is richer in neochlorogenic acid (16‐fold), p‐coumaric acid (5.3‐fold), rutin (2.8‐fold), caffeic acid (1.5‐fold) and cinaroside (1.5‐fold) than the leaves of its parent greenhouse‐cultivated plants. Extracts contained 30 mg/100 g DW of casticin, but after the hydrolysis its amount increased up to 200 mg/100 g DW and twice exceeded the content in the greenhouse leaves. The results indicate that V. agnus castus agitated shoot cultures might be considered as a potential biotechnological source of some pharmaceutically important compounds, especially casticin, rutin, neochlorogenic and p‐coumaric acids.     

Rotavirus VP8*: Phylogeny, Host Range, and Interaction with Histo-Blood Group Antigens

The distal portion of rotavirus (RV) VP4 spike protein (VP8*) is implicated in binding to cellular receptors, thereby facilitating viral attachment and entry. While VP8* of some animal RVs engage sialic acid, human RVs often attach to and enter cells in a sialic acid-independent manner. A recent study demonstrated that the major human RVs (P[4], P[6], and P[8]) recognize human histo-blood group antigens (HBGAs). In this study, we performed a phylogenetic analysis of RVs and showed further variations of RV interaction with HBGAs. On the basis of the VP8* sequences, RVs are grouped into five P genogroups (P[I] to P[V]), of which P[I], P[IV], and P[V] mainly infect animals, P[II] infects humans, and P[III] infects both animals and humans. The sialic acid-dependent RVs (P[1], P[2], P[3], and P[7]) form a subcluster within P[I], while all three major P genotypes of human RVs (P[4], P[6], and P[8]) are clustered in P[II]. We then characterized three human RVs (P[9], P[14], and P[25]) in P[III] and observed a new pattern of binding to the type A antigen which is distinct from that of the P[II] RVs. The binding was demonstrated by hemagglutination and saliva binding assay using recombinant VP8* and native RVs. Homology modeling and mutagenesis study showed that the locations of the carbohydrate binding interfaces are shared with the sialic acid-dependent RVs, although different amino acids are involved. The P[III] VP8* proteins also bind the A antigens of the porcine and bovine mucins, suggesting the A antigen as a possible factor for cross-species transmission of RVs. Our study suggests that HBGAs play an important role in RV infection and evolution.