The structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase

The RNA-dependent RNA polymerase of bacteriophage phi6 transcribes mRNA from the three segments of the dsRNA viral genome. We have cocrystallized RNA oligonucleotides with the polymerase, revealing the mode of binding of RNA templates. This binding is somewhat different from that previously seen for DNA oligomers, leading to additional RNA-protein hydrogen bonds, consistent with a preference for RNA. Activation of the RNA/polymerase complex by the addition of substrate and Mg2+ initiates a single round of reaction within the crystal to form a dead-end complex that partially collapses within the enzyme active site. By replacing Mg2+ with Ca2+, we have been able to capture the inhibited complex which shows distortion that explains the structural basis for the inhibition of such polymerases by Ca2+.     

The Molecular Chaperone HSP70 Binds to and Stabilizes NOD2, an Important Protein Involved in Crohn Disease

Microbes are detected by the pathogen-associated molecular patterns through specific host pattern recognition receptors. Nucleotide-binding oligomerization domain-containing protein 2 (NOD2) is an intracellular pattern recognition receptor that recognizes fragments of the bacterial cell wall. NOD2 is important to human biology; when it is mutated it loses the ability to respond properly to bacterial cell wall fragments. To determine the mechanisms of misactivation in the NOD2 Crohn mutants, we developed a cell-based system to screen for protein-protein interactors of NOD2. We identified heat shock protein 70 (HSP70) as a protein interactor of both wild type and Crohn mutant NOD2. HSP70 has previously been linked to inflammation, especially in the regulation of anti-inflammatory molecules. Induced HSP70 expression in cells increased the response of NOD2 to bacterial cell wall fragments. In addition, an HSP70 inhibitor, KNK437, was capable of decreasing NOD2-mediated NF-κB activation in response to bacterial cell wall stimulation. We found HSP70 to regulate the half-life of NOD2, as increasing the HSP70 level in cells increased the half-life of NOD2, and down-regulating HSP70 decreased the half-life of NOD2. The expression levels of the Crohn-associated NOD2 variants were less compared with wild type. The overexpression of HSP70 significantly increased NOD2 levels as well as the signaling capacity of the mutants. Thus, our study shows that restoring the stability of the NOD2 Crohn mutants is sufficient for rescuing the ability of these mutations to signal the presence of a bacterial cell wall ligand.     

A remote-query sensor for predictive indication of milk spoilage

Described is application of the remote-query (wireless, passive) magnetoelastic sensor platform for direct detection and monitoring of bacterium contamination of milk within hermetically sealed containers. Specific application is made to the quantification of Staphylococcus aureus ssp. anaerobius (S. aureus) concentrations in milk. S. aureus growth changes milk viscosity, in turn changing the resonance frequency of the liquid immersed sensor allowing S. aureus concentrations of 10³ to 10⁷ cells ml⁻¹ to be directly quantified.     

Isolation of a human ceruloplasmin cDNA clone that includes the N-terminal leader sequence

A number of cDNA clones encoding human ceruloplasmin were identified using two mixed oligonucleotide probes. One of these clones was shown by DNA sequence analysis to span from the complete N-terminal leader sequence to 114 amino acids short of the C-terminus. The leader sequence consists of 19 primarily hydrophobic amino acids. Northern blot analysis of RNA from human liver showed two species of ceruloplasmin mRNA; a minor species of 3600 nucleotides and a major one of 4400 nucleotides.     

Anti-tumor antibody produced by human tumor-infiltrating and peripheral blood B lymphocytes

Cell suspensions from 69 human tumor biopsies and malignant effusions depleted of infiltrating T cells were incubated for 10–14 days with mitomycin-C-treated cells of the transformed T cell line MOT as feeder cells. B lymphocytes proliferated and differentiated as indicated by immunoglobulin (Ig) seerction in the culture supernatants (B cell expansion). Ig was present in culture supernatants of tumor cell suspensions incubated without MOT feeder cells (non-expanded cells), but the addition of MOT feeder cells to these cultures invariably resulted in a significant increase in Ig concentration. While IgG, IgA. and IgM isotypes were all detected in supernatants of both expanded- and nonexpanded tumor cell suspensions, the increase in total Ig induced by MOT feeder cells was mainly due to an increase in IgG. Peripheral blood B lymphocytes (PBBL) from 15 cancer patients and 4 healthy individuals were also successfully expanded by the same method. In these it was shown that IgA was the predominant Ig isotype. Using a modified enzyme-linked immunosorbent assay, IgG of 25/36 expansions from tumor cell suspensions showed reactivity with autologous tumor targets, and that from 10/13 expansions reacted with allogeneic tumor targets of the same histological diagnosis. No reactivity was found against tumor targets of different histology. IgG of 4/10 expansions of PBBL from cancer patients showed reactivity with allogeneic tumor targets of the same histology, while no reactivity was demonstrated against tumor targets of different histology. IgG of expanded PBBL from healthy individuals showed no reactivity against tumor targets. This method allows detailed study of the specific humoral antitumor immune response of intratumoral and peripheral blood B lymphocytes in cancer.Work supported by grants from the Share and Concern Foundations and grant CA MOPP from the National Institutes of Health, C.J.A.P. is a visiting scientist from the University of Nijmegen, Department of Medical Oncology, Nijmegen, The Netherlands, and is supported by a Fulbright Senior Research Grant and grants from the Dutch Cancer Society and the Regional Cancer Center of the East Netherlands (IKO). J.A.M.B. is a visiting scientist from the University of Sao Paolo, Department of Immunology, Brazil, and is supported by grant 90/1844-4 from the FAPESP     

String Theory - The Physics of String-Bending and Other Electric Guitar Techniques

Electric guitar playing is ubiquitous in practically all modern music genres. In the hands of an experienced player, electric guitars can sound as expressive and distinct as a human voice. Unlike other more quantised instruments where pitch is a discrete function, guitarists can incorporate micro-tonality and, as a result, vibrato and sting-bending are idiosyncratic hallmarks of a player. Similarly, a wide variety of techniques unique to the electric guitar have emerged. While the mechano-acoustics of stringed instruments and vibrating strings are well studied, there has been comparatively little work dedicated to the underlying physics of unique electric guitar techniques and strings, nor the mechanical factors influencing vibrato, string-bending, fretting force and whammy-bar dynamics. In this work, models for these processes are derived and the implications for guitar and string design discussed. The string-bending model is experimentally validated using a variety of strings and vibrato dynamics are simulated. The implications of these findings on the configuration and design of guitars is also discussed.     

Affinity-dependent cross-linking to neurotoxin sites of the acetylcholine receptor mediated by catechol oxidation

The choline homologue 3-[(trimethylammonio)methyl]catechol (TMC) has been synthesized, and the controllable features of its complex oxidation have been examined spectroscopically and correlated with its toxin binding inactivating reactions with the acetylcholine receptor (AcChR) from Torpedo californica electroplax. Affinity-dependent reactions of early intermediates in the oxidation of TMC are suggested to intercede covalently in this inactivation. At pH 7.4, where the oxidative polymerization of catechols proceeds spontaneously, pyrocatechol produced no effect on the toxin binding function of AcChR, whereas comparable concentrations of TMC led to inactivation of half of all available sites. Lower concentrations of TMC converted via oxidation with ceric salts to an in situ mixture of monohydroxylated catechols were shown to be effective in short-term incubations in inactivating approximately half of the toxin binding sites by covalent labeling of the receptor. Mixtures of dihydroxycatechol intermediates, hydroxy-p-quinones, and polymeric products led to nonspecific toxin binding site inactivation of AcChR in excess of half of all available sites. Collectively, the results suggest that both covalent labeling and oxygen reduction product inactivating mechanisms are operative in these model macromolecular site reactions and that catechol-containing affinity reagents may be useful in elucidating the molecular features of sites to which they are directed.