What reaches the antenna? How to calibrate odor flux and ligand-receptor affinities

Physiological studies on olfaction frequently ignore the airborne quantities of stimuli reaching the sensory organ. We used a gas chromatography-calibrated photoionization detector to estimate quantities released from standard Pasteur pipette stimulus cartridges during repeated puffing of 27 compounds and verified how lack of quantification could obscure olfactory sensory neuron (OSN) affinities. Chemical structure of the stimulus, solvent, dose, storage condition, puff interval, and puff number all influenced airborne quantities. A model including boiling point and lipophilicity, but excluding vapor pressure, predicted airborne quantities from stimuli in paraffin oil on filter paper. We recorded OSN responses of Drosophila melanogaster, Ips typographus, and Culex quinquefasciatus, to known quantities of airborne stimuli. These demonstrate that inferred OSN tuning width, ligand affinity, and classification can be confounded and require stimulus quantification. Additionally, proper dose-response analysis shows that Drosophila AB3A OSNs are not promiscuous, but highly specific for ethyl hexanoate, with other earlier proposed ligands 10- to 10?000-fold less potent. Finally, we reanalyzed published Drosophila OSN data (DoOR) and demonstrate substantial shifts in affinities after compensation for quantity and puff number. We conclude that consistent experimental protocols are necessary for correct OSN classification and present some simple rules that make calibration, even retroactively, readily possible.     

Toll-like receptor 4-mediated signaling by epithelial surfaces: necessity or threat?

Recent data suggest that the lipopolysaccharide receptor Toll-like receptor (TLR) 4 is expressed by epithelial cells and might play a role in the mucosal host defense against Gram-negative bacteria. However, since many body surfaces are colonized by the physiological microflora, activation of epithelial TLRs must be tightly controlled to avoid unintended stimulation and mucosal inflammation. The present review summarizes the current understanding of TLR4-mediated recognition and addresses specific questions on microbial recognition on mucosal surfaces, with particular emphasis on the gastrointestinal and urinary tract.     

Improved Inhibitor Screening Experiments by Comparative Analysis of Simulated Enzyme Progress Curves

A difficulty associated with high throughput screening for enzyme inhibitors is to establish reaction conditions that maximize the sensitivity and resolution of the assay. Deduction of information from end-point assays at single concentrations requires a detailed understanding of the time progress of the enzymatic reaction, an essential but often difficult process to model. A tool to simulate the time progress of enzyme catalyzed reactions and allows adjustment of reactant concentrations and parameters (initial concentrations, K _m, k _cat, K _i values, enzyme half-life, product•enzyme dissociation constant, and the rate constant for the reversed reaction) has been developed. This tool provides comparison of the progress of uninhibited versus inhibited reactions for common inhibitory mechanisms, and guides the tuning of reaction conditions. Possible applications include: analysis of substrate turnover, identification of the point of maximum difference in product concentration (Δ_max[P]) between inhibited and uninhibited reactions, determination of an optimal observation window unbiased for inhibitor mechanisms or potency, and interpretation of observed inhibition in terms of true inhibition. An important observation that can be utilized to improve assay signal strength and resolution is that Δ_max[P] occurs at a high degree of substrate consumption (commonly >75%) and that observation close to this point does not adversely affect observed inhibition or IC₅₀ values.     

Antibodies for profiling the human proteome-The Human Protein Atlas as a resource for cancer research

In this review, we present an update on the progress of the Human Protein Atlas, with an emphasis on strategies for validating immunohistochemistry-based protein expression patterns and on the possibilities to extend the map of protein expression patterns for cancer research projects. The objectives underlying the Human Protein Atlas include (i) the generation of validated antibodies toward a major isoform of all proteins encoded by the human genome, (ii) creating an information database of protein expression patterns in normal human tissues, in cells, and in cancer, and (iii) utilizing generated antibodies and protein expression data as tools to identify clinically useful biomarkers. The success of such an effort is dependent on the validity of antibodies as specific binders of intended targets in applications used to map protein expression patterns. The development of strategies to support specific target binding is crucial and remains a challenge as a large fraction of proteins encoded by the human genome is poorly characterized, including the approximately one-third of all proteins lacking evidence of existence. Conceivable methods for validation include the use of paired antibodies, i.e. two independent antibodies targeting different and nonoverlapping epitopes on the same protein as well as comparative analysis of mRNA expression patterns with corresponding proteins.     

Bandpass filtering of DNA elastic modes using confinement and tension

During a variety of biological and technological processes, biopolymers are simultaneously subject to both confinement and external forces. Although significant efforts have gone into understanding the physics of polymers that are only confined, or only under tension, little work has been done to explore the effects of the interplay of force and confinement. Here, we study the combined effects of stretching and confinement on a polymer's configurational freedom. We measure the elastic response of long double-stranded DNA molecules that are partially confined to thin, nanofabricated slits. We account for the data through a model in which the DNA's short-wavelength transverse elastic modes are cut off by applied force and the DNA's bending stiffness, whereas long-wavelength modes are cut off by confinement. Thus, we show that confinement and stretching combine to permit tunable bandpass filtering of the elastic modes of long polymers.     

Skin Electroporation: Effects on Transgene Expression,DNA Persistence and Local Tissue Environment

Background

Electrical pulses have been used to enhance uptake of molecules into living cells for decades. This technique, often referred to as electroporation, has become an increasingly popular method to enhance in vivo DNA delivery for both gene therapy applications as well as for delivery of vaccines against both infectious diseases and cancer. In vivo electrovaccination (gene delivery followed by electroporation) is currently being investigated in several clinical trials, including DNA delivery to healthy volunteers. However, the mode of action at molecular level is not yet fully understood.

Methodology/Principal Findings

This study investigates intradermal DNA electrovaccination in detail and describes the effects on expression of the vaccine antigen, plasmid persistence and the local tissue environment. Gene profiling of the vaccination site showed that the combination of DNA and electroporation induced a significant up-regulation of pro-inflammatory genes. In vivo imaging of luciferase activity after electrovaccination demonstrated a rapid onset (minutes) and a long duration (months) of transgene expression. However, when the more immunogenic prostate specific antigen (PSA) was co-administered, PSA-specific T cells were induced and concurrently the luciferase expression became undetectable. Electroporation did not affect the long-term persistence of the PSA-expressing plasmid.

Conclusions/Significance

This study provides important insights to how DNA delivery by intradermal electrovaccination affects the local immunological responses of the skin, transgene expression and clearance of the plasmid. As the described vaccination approach is currently being evaluated in clinical trials, the data provided will be of high significance.     

Self-assembly formation of multiple DNA-tethered lipid bilayers

Inspired by natural cell–cell junctions, where membrane-residing proteins control the separation between two or more membranes without interfering with their integrity, we report a new self-assembly route for formation of multiple highly fluid tethered lipid bilayers with the inter-membrane volume geometrically confined by membrane-anchored DNA duplexes. The formation of multiple planar membrane–membrane junctions were accomplished using disk shaped bicelles, composed of a mixture of the long-chained dimyristoyl phosphatidylcholine (DMPC) and the short-chained dihexanoyl PC further stabilized with the positively charged detergent hexadecyl-trimethyl-ammonium bromide (CTAB). Quartz crystal microbalance with dissipation (QCM-D) monitoring and fluorescence microscopy and fluorescence recovery after photobleaching (FRAP) were used to monitor the formation and to characterize the integrity of the self-assembled lipid–DNA architecture.     

Amyloid Formation by the Pro-Inflammatory S100A8/A9 Proteins in the Ageing Prostate

Background

The conversion of soluble peptides and proteins into polymeric amyloid structures is a hallmark of many age-related degenerative disorders, including Alzheimer''s disease, type II diabetes and a variety of systemic amyloidoses. We report here that amyloid formation is linked to another major age-related phenomenon − prostate tissue remodelling in middle-aged and elderly men.

Methodology/Principal Findings

By using multidisciplinary analysis of corpora amylacea inclusions in prostate glands of patients diagnosed with prostate cancer we have revealed that their major components are the amyloid forms of S100A8 and S100A9 proteins associated with numerous inflammatory conditions and types of cancer. In prostate protease rich environment the amyloids are stabilized by dystrophic calcification and lateral thickening. We have demonstrated that material closely resembling CA can be produced from S100A8/A9 in vitro under native and acidic conditions and shows the characters of amyloids. This process is facilitated by calcium or zinc, both of which are abundant in ex vivo inclusions. These observations were supported by computational analysis of the S100A8/A9 calcium-dependent aggregation propensity profiles. We found DNA and proteins from Escherichia coli in CA bodies, suggesting that their formation is likely to be associated with bacterial infection. CA inclusions were also accompanied by the activation of macrophages and by an increase in the concentration of S100A8/A9 in the surrounding tissues, indicating inflammatory reactions.

Conclusions/Significance

These findings, taken together, suggest a link between bacterial infection, inflammation and amyloid deposition of pro-inflammatory proteins S100A8/A9 in the prostate gland, such that a self-perpetuating cycle can be triggered and may increase the risk of malignancy in the ageing prostate. The results provide strong support for the prediction that the generic ability of polypeptide chains to convert into amyloids could lead to their involvement in an increasing number of otherwise apparently unrelated diseases, particularly those associated with ageing.     

Is Genetic Background Important in Lung Cancer Survival?

Background

In lung cancer, a patient''s survival is poor with a wide variation in survival within the stage of disease. The aim of this study was to investigate the familial concordance in lung cancer survival by means of analyses of pairs with different degrees of familial relationships.

Methods

Our population-based Swedish family database included three million families and over 58 100 lung cancer patients. We modelled the proband (parent, sibling, spouse) survival utilizing a multivariate proportional hazard (Cox) model adjusting for possible confounders of survival. Subsequently, the survival in proband''s relative (child, sibling, spouse) was analysed with a Cox model.

Findings

By use of Cox modelling with 5 years follow-up, we noted a decreased hazard ratio for death in children with good parental survival (Hazard Ratio [HR] = 0.71, 95% CI = 0.51 to 0.99), compared to those with poor parental survival. Also for siblings, a very strong protective effect was seen (HR = 0.14, 95% CI = 0.030 to 0.65). Finally, in spouses no correlation in survival was found.

Interpretation

Our findings suggest that genetic factors are important in lung cancer survival. In a clinical setting, information on prognosis in a relative may be vital in foreseeing the survival in an individual newly diagnosed with lung cancer. Future molecular studies enhancing the understanding of the underlying mechanisms and pathways are needed.