Comparison of normal and breast cancer cell lines using proteome, genome, and interactome data

Normal and cancer cell line proteomes were profiled using high throughput mass spectrometry techniques. Application of protein-level and peptide-level sample fractionation combined with LC-MS/MS analysis enabled identification of 2235 unmodified proteins representing a broad range of functional and compartmental classes. An iterative multistep search strategy was used to identify post-translational modifications, revealing several proteins that are preferentially modified in cancer cells. Information regarding both unmodified and modified protein forms was combined with publicly available gene expression and protein-protein interaction data. The resulting integrated dataset revealed several functionally related proteins that are differentially regulated between normal and cancer cell lines.     

Growth rate and oxygen regulate the interactions of group B Streptococcus with polarized respiratory epithelial cells

We investigated growth conditions that regulate the ability of group B Streptococcus (GBS) to attach to, invade, and translocate through polarized human respiratory epithelial cells (RECs). GBS grown in a chemostat at a fast cell mass doubling time (t(d) = 1.8 h), invaded RECs from both the apical and basolateral surfaces in higher numbers compared with those held at a t(d) = 11 h. With the exception of adherence from the basolateral surface, GBS reached peak adherence to, invasion of, and translocation through RECs when held at the fast t(d) with 15% dissolved oxygen compared with 0% dissolved oxygen. Growth rate and oxygen level strongly influence the interaction of GBS with polarized RECs and likely GBS pathogenicity.     

Acceleration of early chick embryo morphogenesis by insulin is associated with altered expression of embryonic genes

In the present study, we show that insulin accelerates early morphogenesis in gastrulating chick embryo explants cultured in vitro, whereas antiserum to insulin adversely affects this process. Comparison between length of body axis of control and treated embryos clearly brings out the significant acceleration of development by excess insulin (0.175 to 17.5 nM). In embryos treated with 87.5 and 175 nM insulin, a high occurrence of abnormalities is observed. Treatment of embryos with antiserum to porcine insulin results in a high percentage of abnormalities, particularly in the forming neural tube. In situ hybridization of whole embryos using digoxigenin-labeled riboprobes showed that insulin modifies the expression of crucial developmental genes within 2 hours. While Brachyury, a pan-mesodermal marker gene, ERNI, the earliest known marker for neural induction in chick, and noggin, important in neural tube patterning, are upregulated, expression of goosecoid, necessary for gastrulation movements, does not appear to be significantly altered. During the same time, insulin does not exert any mitogenic effect on chick embryonic cells as assessed by nuclear counts. These findings demonstrate that insulin plays an important role in the early morphogenesis of the chick embryo. The function of insulin appears to be mediated by specific genes which orchestrate pattern formation during early development.     

Ablation surgery for atrial fibrillation: "freeze it or buzz it; just do it and cure it"

Patients in normal sinus rhythm have lesser stroke rate, better functional class and quality of life than those in atrial fibrillation. Adding a surgical procedure to cure atrial fibrillation in patients needing correction of structural heart disease has been shown to be a safe option, which benefits the majority in restoration of sinus rhythm. Age is no bar to implement this option. The same does not hold true for lone atrial fibrillation. The affirm trial has shown that there is need for improved treatment strategies for patients in atrial fibrillation, although young patients were not represented in sizable proportion. There is need to develop curative treatment for patients with lone atrial fibrillation. And there are technological advances in the form of ablative energy sources and hardware for applying these with minimal invasion. "Between tomorrow's dream and yesterday's regret is today's opportunity". Let's make the best of it!     

Functional Gene Hybridization Patterns of Terrestrial Ammonia-Oxidizing Bacteria

Abstract The biochemical pathway and genetics of autotrophic ammonia oxidation have been studied almost exclusively in Nitrosomonas europaea. Terrestrial autotrophic ammonia-oxidizing bacteria (AAOs), however, comprise two distinct phylogenetic groups in the beta-Proteobacteria, the Nitrosomonas and Nitrosospira groups. Hybridization patterns were used to assess the potential of functional probes in non-PCR-based molecular analysis of natural AAO populations and their activity. The objective of this study was to obtain an overview of functional gene homologies by hybridizing probes derived from N. europaea gene sequences ranging in size from 0.45 to 4.5 kb, and labeled with 32P to Southern blots containing genomic DNA from four Nitrosospira representatives. Probes were specific for genes encoding ammonia monooxygenase (amoA and amoB), hydroxylamine oxidoreductase (hao), and cytochrome c-554 (hcy). These probes produced hybridization signals, at low stringency (30 degreesC), with DNA from each of the four representatives; signals at higher stringency (42 degreesC) were greatly reduced or absent. The hybridization signals at low stringency ranged from 20 to 76% of the total signal obtained with N. europaea DNA. These results indicate that all four functional genes in the ammonia oxidation pathway have diverged between the Nitrosomonas and Nitrosospira groups. The hao probe produced the most consistent hybridization intensities among the Nitrosospira representatives, suggesting that hao sequences would provide the best probes for non-PCR-based molecular analysis of terrestrial AAOs. Since N. europaea can also denitrify, an additional objective was to hybridize genomic DNA from AAOs with probes for Pseudomonas genes involved in denitrification. These probes were specific for genes encoding heme-type dissimilatory nitrite reductase (dNir), Cu-type dNir, and nitrous oxide reductase (nosz). No hybridization signals were observed from probes for the heme-type dNir or nosz, but Nitrosospira sp. NpAV and Nitrosolobus sp. 24-C hybridized, under low-stringency conditions, with the Cu-type dNir probe. These results indicate that AAOs may also differ in their mechanisms and capacities for denitrification.     

ACG, the initiator codon for a Sendai virus protein

Deletion and site-directed point mutants of the polycistronic P/C mRNA of Sendai virus revealed that one of the nonstructural proteins of this virus, the C' protein, initiates from an ACG codon. This ACG codon occurs in an optimum sequence context and precedes the first AUG of the P/C mRNA. The results presented in this communication are consistent with the concept that the ribosomes scan the P/C mRNA to initiate several proteins from its different initiator codons. The arrangement of several weak initiator codons in tandem in an mRNA, i.e. non-AUG in optimum sequence context and AUG in suboptimum sequence context, may represent an alternate means to regulate gene expression in eukaryotes and their viruses.     

Frequency of micronuclei in peripheral blood lymphocytes from subjects occupationally exposed to low levels of ionizing radiation

The aim of this study was to evaluate the genotoxic effect of low dose of occupational radiation exposure in Nuclear Medicine Department employees, by using cytokinesis-blocked micronucleus assay in peripheral blood lymphocytes. The study included 46 exposed individuals together with 27 from the same area without occupational exposure to radiation which served as controls. The results obtained were evaluated with respect to age, gender, smoking habits, pathological condition and the occupational exposure to radiation of the individuals. The frequency of micronuclei increased significantly with the age of the subjects (P = 0.007). However there were no significant differences in micronucleus frequency with gender, smoking habits and occupational exposure. The frequency of micronuclei was significantly higher in individuals with presence of pathological condition (P < 0.0001) in comparison to healthy population irrespective of their exposure status.     

Structural studies of the archaeal MCM complex in different functional states

The primary candidate for the eukaryotic replicative helicase is the MCM2-7 complex, a hetero-oligomer formed by six AAA+ paralogous polypeptides. A simplified model for structure-function studies is the homo-oligomeric orthologue from the archaeon Methanothermobacter thermoautotrophicus. The crystal structure of the DNA-interacting N-terminal domain of this homo-oligomer revealed a double hexamer in a head-to-head configuration; single-particle electron microscopy studies have shown that the full-length protein complex can form both single and double rings, in which each ring can consist of a cyclical arrangement of six or seven subunits. Using single-particle techniques and especially multivariate statistical symmetry analysis, we have assessed the changes in stoichiometry that the complex undergoes when treated with various nucleotide analogues or when binding a double-stranded DNA fragment. We found that the binding of nucleotides or of double-stranded DNA leads to the preferred formation of double-ring structures. Specifically, the protein complex is present as a double heptamer when treated with a nucleotide analogue, but it is rather found as a double hexamer when complexed with double-stranded DNA. The possible physiological role of the various stoichiometries of the complex is discussed in the light of the proposed mechanisms of helicase activity.     

Phage-Displayed Libraries for the Selection of Optimal Affinity Peptides for Protein Purification Using Ni-Nitrilotriacetic Acid Chromatography

A random hexapeptide library, cloned in bacteriophage, was used to select affinity peptides using nickel-nitrilotriacetic acid (Ni-NTA) columns. The screening protocol was successful by isolating peptides sharing common features and, in most cases, common amino acid sequences were isolated (e.g. WHHHPH, AQHHHH). Ni-NTA chromatography of the fusion phage of the selected peptides exhibited a more homogeneous elution behavior (i.e. elution in one peak) than the most commonly used His₆peptide (elution in multiple peaks).     

OMERO: flexible, model-driven data management for experimental biology

Data-intensive research depends on tools that manage multidimensional, heterogeneous datasets. We built OME Remote Objects (OMERO), a software platform that enables access to and use of a wide range of biological data. OMERO uses a server-based middleware application to provide a unified interface for images, matrices and tables. OMERO's design and flexibility have enabled its use for light-microscopy, high-content-screening, electron-microscopy and even non-image-genotype data. OMERO is open-source software, available at http://openmicroscopy.org/.