Protonation controls ASIC1a activity via coordinated movements in multiple domains.

Acid-sensing ion channels (ASICs) are neuronal Na(+)-conducting channels activated by extracellular acidification. ASICs are involved in pain sensation, expression of fear, and neurodegeneration after ischemic stroke. Functional ASICs are composed of three identical or homologous subunits, whose extracellular part has a handlike structure. Currently, it is unclear how protonation of residues in extracellular domains controls ASIC activity. Knowledge of these mechanisms would allow a rational development of drugs acting on ASICs. Protonation may induce conformational changes that control the position of the channel gate. We used voltage-clamp fluorometry with fluorophores attached to residues in different domains of ASIC1a to detect conformational changes. Comparison of the timing of fluorescence and current signals identified residues involved in movements that preceded desensitization and may therefore be associated with channel opening or early steps leading to desensitization. Other residues participated in movements intimately linked to desensitization and recovery from desensitization. Fluorescence signals of all mutants were detected at more alkaline pH than ionic currents. Their midpoint of pH dependence was close to that of steady-state desensitization, whereas the steepness of the pH fluorescence relationship was closer to that of current activation. A sequence of movements was observed upon acidification, and its backward movements during recovery from desensitization occurred in the reverse order, indicating that the individual steps are interdependent. Furthermore, the fluorescence signal of some labeled residues in the finger domain was strongly quenched by a Trp residue in the neighboring β-ball domain. Upon channel activation, their fluorescence intensity increased, indicating that the finger moved away from the β ball. This extensive analysis of activity-dependent conformational changes in ASICs sheds new light on the mechanisms by which protonation controls ASIC activity

A promising new ELISA diagnostic test for cattle babesiosis based on Babesia bigemina Apical Membrane Antigen-1.

Babesiosis due to Babesia bigemina is a relevant tick‑borne disease, affecting cattle worldwide. Many surface proteins of the pathogen including the Apical Membrane Antigen 1 (AMA‑1) ‑ have been analysed for vaccine and diagnostic purposes. This study focused on B. bigemina AMA‑1 and on its use for the assessment of diagnostic tests. After bioinformatic analyses, AMA‑1 codifying region was amplified and cloned into an expression vector used to induce protein synthesis in Escherichia coli cells. AMA‑1 was purified by affinity chromatography and used to set up the best condition for an ELISA protocol. Bovine field sera positive to B. bigemina were used to evaluate the presence of anti‑AMA‑1 antibodies. In order to verify the assay specificity, sera positive to Babesia bovis or to the piroplasm Theileria annulata were also included. Significant differences were obtained between sera negative to both B. bigemina and B. bovis and samples positive to B. bigemina, to B. bovis or to both pathogens. No significant reaction was observed with T. annulata positive sera. The results showed that AMA‑1 protein is suitable to be used as antigen in diagnostic assays for babesiosis diagnosis in cattle, as it does not show any cross reaction with anti-T. annulata antibodies

Overcoming Language Dichotomies: Toward Effective Program Comprehension for Mobile App Development

Mobile devices and platforms have become an established target for modern software developers due to performant hardware and a large and growing user base numbering in the billions. Despite their popularity, the software development process for mobile apps comes with a set of unique, domain-specific challenges rooted in program comprehension. Many of these challenges stem from developer difficulties in reasoning about different representations of a program, a phenomenon we define as a "language dichotomy". In this paper, we reflect upon the various language dichotomies that contribute to open problems in program comprehension and development for mobile apps. Furthermore, to help guide the research community towards effective solutions for these problems, we provide a roadmap of directions for future work.Comment: Invited Keynote Paper for the 26th IEEE/ACM International Conference on Program Comprehension (ICPC'18

Similarities and differences between molecular order in the nematic and twist-bend nematic phases of a symmetric liquid crystal dimer

The order parameter, Szz, where z is the para axis of the difluoroterphenyl groups in DTC5C9, have been obtained from chemical shift anisotropies measured by ¹³C – {¹1H} NMR experiments at temperatures throughout the nematic, NU, and twist-bend nematic, NTB, phases shown by this compound. The order parameter temperature profiles are unusual in having a maximum value in the NU phase and then decreasing until the NTB phase is reached. There is a small discontinuity (~2%) in Szz at T_(NN_TB )and then a gradual decrease until a new phase appears. This behaviour is interpreted as revealing a temperature-dependent tilting of local directors in both phases away from the applied magnetic field direction. In the enantiomorphic twist-bend phase this tilt is consistent with the structure of the phase as a helical arrangement of local directors, whilst in the high-temperature non-chiral nematic the tilt must involve a non-chiral arrangement. It is proposed that in both phases the tilting of directors has a common origin in the bent shape of the molecules

Automatic Detection of GUI Design Smells: The Case of Blob Listener

International audienceGraphical User Interfaces (GUIs) intensively rely on event-driven programming: widgets send GUI events, which capture users' interactions, to dedicated objects called controllers. Controllers implement several GUI listeners that handle these events to produce GUI commands. In this work, we conducted an empirical study on 13 large Java Swing open-source software systems. We study to what extent the number of GUI commands that a GUI listener can produce has an impact on the change-and fault-proneness of the GUI listener code. We identify a new type of design smell, called Blob listener that characterizes GUI listeners that can produce more than two GUI commands. We show that 21 % of the analyzed GUI controllers are Blob listeners. We propose a systematic static code analysis procedure that searches for Blob listener that we implement in InspectorGuidget. We conducted experiments on six software systems for which we manually identified 37 instances of Blob listener. InspectorGuidget successfully detected 36 Blob listeners out of 37. The results exhibit a precision of 97.37 % and a recall of 97.59 %. Finally, we propose coding practices to avoid the use of Blob listeners

Massive star cluster formation and evolution in tidal dwarf galaxies

Reproduced with permission from Astronomy & Astrophysics. © 2019 ESOThe formation of globular clusters remains an open debate. Dwarf starburst galaxies are efficient at forming young massive clusters with similar masses as globular clusters and may hold the key to understanding their formation. We study star cluster formation in a tidal debris - including the vicinity of three tidal dwarf galaxies - in a massive gas dominated collisional ring around NGC~5291. These dwarfs have physical parameters which differ significantly from local starbursting dwarfs. They are gas-rich, highly turbulent, have a gas metallicity already enriched up to half-solar, and are expected to be free of dark matter. The aim is to study massive star cluster formation in this as yet unexplored type of environment. We use imaging from the Hubble Space Telescope using broadband filters covering the wavelength range from the near-ultraviolet to the near-infrared. We determine the masses and ages of the cluster candidates by using the spectral energy distribution-fitting code CIGALE, carefully considering age-extinction degeneracy effects on the estimation of the physical parameters. We find that the tidal dwarf galaxies in the ring of NGC 5291 are forming star clusters with an average efficiency of $\sim40\%$, comparable to blue compact dwarf galaxies. We also find massive star clusters for which the photometry suggests that they were formed at the very birth of the tidal dwarf galaxies and have survived for several hundred million years. Therefore our study shows that extended tidal dwarf galaxies and compact clusters may be formed simultaneously. In the specific case observed here, the young star clusters are not massive enough to survive for a Hubble time. However one may speculate that similar objects at higher redshift, with higher star formation rate, might form some of the long lived globular clusters.Peer reviewedFinal Accepted Versio

An Allosteric Cross-Talk Between the Activation Loop and the ATP Binding Site Regulates the Activation of Src Kinase

Phosphorylation of the activation loop is a fundamental step in the activation of most protein kinases. In the case of the Src tyrosine kinase, a prototypical kinase due to its role in cancer and its historic importance, phosphorylation of tyrosine 416 in the activation loop is known to rigidify the structure and contribute to the switch from the inactive to a fully active form. However, whether or not phosphorylation is able per-se to induce a fully active conformation, that efficiently binds ATP and phosphorylates the substrate, is less clear. Here we employ a combination of solution NMR and enhanced-sampling molecular dynamics simulations to fully map the effects of phosphorylation and ATP/ADP cofactor loading on the conformational landscape of Src tyrosine kinase. We find that both phosphorylation and cofactor binding are needed to induce a fully active conformation. What is more, we find a complex interplay between the A-loop and the hinge motion where the phosphorylation of the activation-loop has a significant allosteric effect on the dynamics of the C-lobe

Changes in the folding landscape of the WW domain provide a molecular mechanism for an inherited genetic syndrome

WW domains are small domains present in many human proteins with a wide array of functions and acting through the recognition of proline-rich sequences. The WW domain belonging to polyglutamine tract-binding protein 1 (PQBP1) is of particular interest due to its direct involvement in several X chromosome-linked intellectual disabilities, including Golabi-Ito-Hall (GIH) syndrome, where a single point mutation (Y65C) correlates with the development of the disease. The mutant cannot bind to its natural ligand WBP11, which regulates mRNA processing. In this work we use high-field high-resolution NMR and enhanced sampling molecular dynamics simulations to gain insight into the molecular causes the disease. We find that the wild type protein is partially unfolded exchanging among multiple beta-strand-like conformations in solution. The Y65C mutation further destabilizes the residual fold and primes the protein for the formation of a disulphide bridge, which could be at the origin of the loss of function

String Theoretical Interpretation for Finite N Yang-Mills Theory in Two-Dimensions

We discuss the equivalence between a string theory and the two-dimensional Yang-Mills theory with SU(N) gauge group for finite N. We find a sector which can be interpreted as a sum of covering maps from closed string world-sheets to the target space, whose covering number is less than N. This gives an asymptotic expansion of 1/N whose large N limit becomes the chiral sector defined by D.Gross and W.Taylor. We also discuss that the residual part of the partition function provides the non-perturbative corrections to the perturbative expansion.Comment: 15 pages, no figures, LaTeX2e, typos corrected, final version to appear in Modern Physics Letters

West Nile virus transmission. results from the integrated surveillance system in Italy, 2008 to 2015

IIn Italy a national Plan for the surveillance of imported and autochthonous human vector-borne diseases (chikungunya, dengue, Zika virus disease and West Nile virus (WNV) disease) that integrates human and veterinary (animals and vectors) surveillance, is issued and revised annually according with the observed epidemiological changes. Here we describe results of the WNV integrated veterinary and human surveillance systems in Italy from 2008 to 2015. A real time data exchange protocol is in place between the surveillance systems to rapidly identify occurrence of human and animal cases and to define and update the map of affected areas i.e. provinces during the vector activity period from June to October. WNV continues to cause severe illnesses in Italy during every transmission season, albeit cases are sporadic and the epidemiology varies by virus lineage and geographic area. The integration of surveillance activities and a multidisciplinary approach made it possible and have been fundamental in supporting implementation of and/or strengthening preventive measures aimed at reducing the risk of transmission of WNV trough blood, tissues and organ donation and to implementing further measures for vector control