Formalizing Program Equivalences in Dependent Type Theory

This brief note summarizes our formalization in a dependently typed setting of the meta-theory of several notions of program equivalences in higher-order programming languages

Kinetic study of two pentameric ligand-gated ion channels

The Cys-loop or nicotinic superfamily is an important group of ligand-gated ion channels. The pentameric channels in this family commonly mediate fast synaptic transmission in eukaryotes (cf. nicotinic acetylcholine, γ-aminobutyric acid receptor and glycine receptor). Related channels are also found in prokaryotes and these channels include Gloeobacter violaceous ligand-gated ion channel (GLIC) and Erwinia chrysanthemi ligand gated ion channel (ELIC). Cys-loop channels share a common structural fold and are thought to activate in a similar way: the ligand binds at the interface between the extracellular domains of adjacent subunits and causes the receptor to undergo a conformational change. This is conveyed to the transmembrane region of the receptor where it results in the opening of the channel pore. The energy landscape of the channel protein can be characterised by determining a kinetic mechanism, which explicitly details the functional states that the channel can visit and quantifies the transition rates between them. This is possible in ion channels because the current generated by a single channel molecule can be detected with high temporal resolution. Establishing a detailed kinetic mechanism allows a better understanding of the structure function relation for the protein, because it allows us to determine which step of the activation is affected when we change agonist or when we mutate the channel protein itself. The aim of my work was to establish the kinetic mechanism that best describes two homomeric ligand-gated ion channels, the α3 glycine receptor and ELIC receptor. This work involved recording single channel currents and the currents elicited by fast agonist applications and analysis by direct model fitting to the data. The physiological role of α3 glycine receptor is not currently known. The α3 expression is concentrated in areas involved in pain processing, such as the superficial dorsal horn (Harvey et al., 2004), suggesting that this isoform could be involved in the nociceptive pathway. Characterising the kinetics of a synaptic receptor is important also in understanding synaptic transmission, because it is the lifetime of the activated channel that is largely responsible for setting the time course of synaptic currents. We investigated the activation mechanism of this channel in HEK293 cells by maximum likelihood fitting of single-channel data, at a wide range of glycine concentrations. The mechanism we propose suggests that α3 channels can open only when more than 3 binding sites are occupied by glycine, and only after the channel undergoes a conformational change (‘flip’) that links binding to gating. The scheme can describe adequately macroscopic currents from fast concentration jumps experiments. The function of the prokaryotic channel ELIC is unknown, but ELIC is important as it has been recently crystallized (Hilf and Dutzler, 2008) in non-conductive state (the highest resolution structure currently available for a non-conductive state). Establishing a kinetic mechanism for this channel is particularly important, because combining structure and function offers the best possibility to investigate how the perturbation induced by the binding of the transmitter opens the channel. We investigated the activation mechanism of this channel in HEK293 cells by maximum likelihood fitting of single-channel data, at a wide range of propylamine concentrations. The mechanism we propose suggests that ELIC can open from partially primed conformational states, and only after the channel undergoes a conformational change (‘priming’), which links binding to gating. The scheme describes adequately both macroscopic currents from fast concentration jumps experiments and single channel activity

Mechanism of activation of the prokaryotic channel ELIC by propylamine: A single-channel study.

Prokaryotic channels, such as Erwinia chrysanthemi ligand-gated ion channel (ELIC) and Gloeobacter violaceus ligand-gated ion channel, give key structural information for the pentameric ligand-gated ion channel family, which includes nicotinic acetylcholine receptors. ELIC, a cationic channel from E. chrysanthemi, is particularly suitable for single-channel recording because of its high conductance. Here, we report on the kinetic properties of ELIC channels expressed in human embryonic kidney 293 cells. Single-channel currents elicited by the full agonist propylamine (0.5-50 mM) in outside-out patches at -60 mV were analyzed by direct maximum likelihood fitting of kinetic schemes to the idealized data. Several mechanisms were tested, and their adequacy was judged by comparing the predictions of the best fit obtained with the observable features of the experimental data. These included open-/shut-time distributions and the time course of macroscopic propylamine-activated currents elicited by fast theta-tube applications (50-600 ms, 1-50 mM, -100 mV). Related eukaryotic channels, such as glycine and nicotinic receptors, when fully liganded open with high efficacy to a single open state, reached via a preopening intermediate. The simplest adequate description of their activation, the "Flip" model, assumes a concerted transition to a single intermediate state at high agonist concentration. In contrast, ELIC open-time distributions at saturating propylamine showed multiple components. Thus, more than one open state must be accessible to the fully liganded channel. The "Primed" model allows opening from multiple fully liganded intermediates. The best fits of this type of model showed that ELIC maximum open probability (99%) is reached when at least two and probably three molecules of agonist have bound to the channel. The overall efficacy with which the fully liganded channel opens was ∼102 (∼20 for α1β glycine channels). The microscopic affinity for the agonist increased as the channel activated, from 7 mM for the resting state to 0.15 mM for the partially activated intermediate state

The restoration of the Colosso di Barletta: EDXRF analysis

The Colosso di Barletta is an imposing outdoor bronze statue, dating back the V century, located near the Basilica of “Santo Sepolcro” in Barletta (Apulia, Southern Italy). The monument underwent a structural restoration in 1981, during which the Central Institute of Restoration in Rome performed cleaning treatments and consolidation of the patinas. Currently, the Laboratory of Archaeometry of the University of Salento is carrying on a campaign of non-destructive and in situ measurements by using energy dispersion X-ray fluorescence (EDXRF) in order to assess the chemical composition of the alloy and to study its patinas

Inhibition of the prokaryotic pentameric ligand-gated ion channel ELIC by divalent cations.

The modulation of pentameric ligand-gated ion channels (pLGICs) by divalent cations is believed to play an important role in their regulation in a physiological context. Ions such as calcium or zinc influence the activity of pLGIC neurotransmitter receptors by binding to their extracellular domain and either potentiate or inhibit channel activation. Here we have investigated by electrophysiology and X-ray crystallography the effect of divalent ions on ELIC, a close prokaryotic pLGIC homologue of known structure. We found that divalent cations inhibit the activation of ELIC by the agonist cysteamine, reducing both its potency and, at higher concentrations, its maximum response. Crystal structures of the channel in complex with barium reveal the presence of several distinct binding sites. By mutagenesis we confirmed that the site responsible for divalent inhibition is located at the outer rim of the extracellular domain, at the interface between adjacent subunits but at some distance from the agonist binding region. Here, divalent cations interact with the protein via carboxylate side-chains, and the site is similar in structure to calcium binding sites described in other proteins. There is evidence that other pLGICs may be regulated by divalent ions binding to a similar region, even though the interacting residues are not conserved within the family. Our study provides structural and functional insight into the allosteric regulation of ELIC and is of potential relevance for the entire family

Synergic combination of the sol-gel method with dip coating for plasmonic devices

Biosensing technologies based on plasmonic nanostructures have recently attracted significant attention due to their small dimensions, low-cost and high sensitivity but are often limited in terms of affinity, selectivity and stability. Consequently, several methods have been employed to functionalize plasmonic surfaces used for detection in order to increase their stability. Herein, a plasmonic surface was modified through a controlled, silica platform, which enables the improvement of the plasmonic-based sensor functionality. The key processing parameters that allow for the fine-tuning of the silica layer thickness on the plasmonic structure were studied. Control of the silica coating thickness was achieved through a combined approach involving sol-gel and dip-coating techniques. The silica films were characterized using spectroscopic ellipsometry, contact angle measurements, atomic force microscopy and dispersive spectroscopy. The effect of the use of silica layers on the optical properties of the plasmonic structures was evaluated. The obtained results show that the silica coating enables surface protection of the plasmonic structures, preserving their stability for an extended time and inducing a suitable reduction of the regeneration time of the chip

Existence of Heavy Fermions in the Antiferromagnetic Phase of CeIn3

We report the pressure-dependent optical conductivity spectra of a heavy fermion (HF) compound CeIn3 below the Neel temperature of 10 K to investigate the existence of the HF state in the antiferromagnetic (AFM) phase. The peak due to the interband transition in the hybridization gap between the conduction band and nearly localized 4f states (c-f hybridization) appears at the photon energy of about 20 meV not only in the HF regime but also in the AFM regime. Both the energy and intensity of the c-f hybridization peak continuously increase with the application of pressure from the AFM to the HF regime. This result suggests that the c-f hybridization, as well as the heavy fermions, exists even in the AFM phase of CeIn3.Comment: 5 pages, 3 figure

Prevalence of Salmonella enterica and Listeria monocytogenes contamination in foods of animal origin in Italy.

The present survey collected and analyzed the results of routine testing for Salmonella enterica and Listeria monocytogenes on foods of animal origin submitted for official controls in Italy during 2001 to 2002. Salmonella was detected in 2.2% of 71,643 food samples examined, and the isolation rates ranged from 9.9% for raw poultry meat to less than 0.1% for dairy products. Isolation rates were also high in raw pork (4.9%) and processed meats (5.3%), which often involved pork. Low rates were observed in seafood (0.5%) and in ready-to-eat foods, such as grocery products (0.7%) and ice creams (0.1%). Serotyping showed that approximately 50% of the isolates belonged to the serotypes most commonly isolated from humans in Italy, thus confirming that most cases of human salmonellosis have a foodborne origin. Levels of L. monocytogenes were higher than what is accepted by the current regulation in 2.4% of 42,300 food samples. The positivity rates ranged from 10.3% in raw pork to none in eggs and egg products. Contamination rates were higher in other meat products (between 2 and 5%) and fish (6.5%) than in cheeses (1.1%) and other dairy products (0.6%). Routine control activities on the microbial contamination of foods can generate data with statistical and epidemiological value. Such data can be used as a basis for estimating the exposure of consumers to foodborne pathogens, following the trends of contamination over time, and evaluating the effects of control measures on the contamination of food

Optical study of the electronic phase transition of strongly correlated YbInCu_4

Infrared, visible and near-UV reflectivity measurements are used to obtain conductivity as a function of temperature and frequency in YbInCu_4, which exhibits an isostructural phase-transition into a mixed-valent phase below T_v=42 K. In addition to a gradual loss of spectral weight with decreasing temperature extending up to 1.5 eV, a sharp resonance appears at 0.25 eV in the mixed-valent phase. This feature can be described in terms of excitations into the Kondo (Abrikosov-Suhl) resonance, and, like the sudden reduction of resistivity, provides a direct reflection of the onset of coherence in this strongly correlated electron system.Comment: 4 pages, 3 figures (to appear in Phys. Rev. B

Correlation gap in the heavy-fermion antiferromagnet UPd_2Al_3

The optical properties of the heavy-fermion compound UPd$_2$Al$_3$ have been measured in the frequency range from 0.04 meV to 5 meV (0.3 to 40 cm$^{-1}$) at temperatures $2 {\rm K}<T< 300$ K. Below the coherence temperature $T^*\approx 50$ K, the hybridization gap opens around 10 meV. As the temperature decreases further ($T\leq 20$ K), a well pronounced pseudogap of approximately 0.2 meV develops in the optical response; we relate this to the antiferromagnetic ordering which occurs below $T_N\approx 14$ K. The frequency dependent mass and scattering rate give evidence that the enhancement of the effective mass mainly occurs below the energy which is associated to the magnetic correlations between the itinerant and localized 5f electrons. In addition to this correlation gap, we observe a narrow zero-frequency conductivity peak which at 2 K is less than 0.1 meV wide, and which contains only a fraction of the delocalized carriers. The analysis of the spectral weight infers a loss of kinetic energy associated with the superconducting transition.Comment: RevTex, 15 pages, 7 figure