RND efflux pumps: structural information translated into function and inhibition mechanisms

Efflux pumps of the Resistance Nodulation Division (RND) superfamily play a major role in the intrinsic and acquired resistance of Gram-negative pathogens to antibiotics. Moreover, they are largely responsible for multi-drug resistance (MDR) phenomena in these bacteria. The last decade has seen a sharp increase in the number of experimental and computational studies aimed at understanding their functional mechanisms. Most of these studies focused on the RND drug/proton antiporter AcrB, part of the AcrAB-TolC efflux pump actively recognizing and expelling noxious agents from the interior of bacteria. These studies have been focused on the dynamical interactions between AcrB and its substrates and inhibitors, on the details of the proton translocation mechanisms, and on the way AcrB assembles with protein partners to build up a functional pump. In this review we summarize these advances focusing on the role of AcrB

Developing an ML pipeline for asthma and COPD: The case of a Dutch primary care service

A complex combination of clinical, demographic and lifestyle parameters determines the correct diagnosis and the most effective treatment for asthma and Chronic Obstructive Pulmonary Disease patients. Artificial Intelligence techniques help clinicians in devising the correct diagnosis and designing the most suitable clinical pathway accordingly, tailored to the specific patient conditions. In the case of machine learning (ML) approaches, availability of real-world patient clinical data to train and evaluate the ML pipeline deputed to assist clinicians in their daily practice is crucial. However, it is common practice to exploit either synthetic data sets or heavily preprocessed collections cleaning and merging different data sources. In this paper, we describe an automated ML pipeline designed for a real-world data set including patients from a Dutch primary care service, and provide a performance comparison of different prediction models for (i) assessing various clinical parameters, (ii) designing interventions, and (iii) defining the diagnosis

Higher and lower supramolecular orders for the design of self-assembled heterochiral tripeptide hydrogel biomaterials

The self-assembly behaviour of the eight stereoisomers of Val\u2013Phe\u2013Phe tripeptides under physiological conditions is assessed by several spectroscopy and microscopy techniques. We report the first examples of self-organised hydrogels from tripeptides in the L\u2013D\u2013L or D\u2013L\u2013D configuration, besides the expected gels with the D\u2013L\u2013L or L\u2013D\u2013D configuration, thus widening the scope for using amino acid chirality as a tool to drive self-assembly. Importantly, the positions of D- and L-amino acids in the gelling tripeptides determine a higher or lower supramolecular order, which translates into macroscopic gels with different rheological properties and thermal behaviours. The more durable hydrogels perform well in cytotoxicity assays, and also as peptides in solution. An appropriate design of the chirality of self-assembling sequences thus allows for the fine-tuning of the properties of the gel biomaterials. In conclusion, this study adds key details of supramolecular organization that will assist in the ex novo design of assembling chiral small molecules for their use as biomaterials

Design of a hydrophobic tripeptide that self-assembles into amphiphilic superstructures forming a hydrogel biomaterial

We report the rational design of a heterochiral hydrophobic tripeptide self-assembling into amphiphilic D-superstructures that yield a self-supportive hydrogel at physiological pH. The material endures cell culture conditions and sustains fibroblast proliferation. Tripeptide superstructures are thoroughly analysed by several techniques

Nanoscale Assembly of Functional Peptides with Divergent Programming Elements

Self-assembling peptides are being applied both in the biomedical area and as building blocks in nanotechnology. Their applications are closely linked to their modes of self-assembly, which determine the functional nanostructures that they form. This work brings together two structural elements that direct nanoscale self-association in divergent directions: proline as a β-breaker and the β-structure-associated diphenylalanine motif, into a single tripeptide sequence. Amino acid chirality was found to resolve the tension inherent to these conflicting self-assembly instructions. Stereoconfiguration determined the ability of each of the eight possible Pro-Phe-Phe stereoisomers to self-associate into diverse nanostructures, including nanoparticles, nanotapes, or fibrils, which yielded hydrogels with gel-to-sol transition at a physiologically relevant temperature. Three single-crystal structures and all-atom molecular dynamics simulations elucidated the ability of each peptide to establish key interactions to form long-range assemblies (i,e., stacks leading to gelling fibrils), medium-range assemblies (i.e., stacks yielding nanotapes), or short-range assemblies (i.e., dimers or trimers that further associated into nanoparticles). Importantly, diphenylalanine is known to serve as a binding site for pathological amyloids, potentially allowing these heterochiral systems to influence the fibrillization of other biologically relevant peptides. To probe this hypothesis, all eight Pro-Phe-Phe stereoisomers were tested in vitro on the Alzheimer's disease-associated Aβ(1-42) peptide. Indeed, one nonfibril-forming stereoisomer effectively inhibited Aβ fibrillization through multivalent binding between diphenylalanine motifs. This work thus defined heterochirality as a useful feature to strategically develop future therapeutics to interfere with pathological processes, with the additional value of resistance to protease-mediated degradation and biocompatibility

Heterochirality and Halogenation Control Phe-Phe Hierarchical Assembly

Diphenylalanine is an amyloidogenic building block that can form a versatile array of supramolecular materials. Its shortcomings, however, include the uncontrolled hierarchical assembly into microtubes of heterogeneous size distribution and well-known cytotoxicity. This study rationalized heterochirality as a successful strategy to address both of these pitfalls and it provided an unprotected heterochiral dipeptide that self-organized into a homogeneous and optically clear hydrogel with excellent ability to sustain fibroblast cell proliferation and viability. Substitution of one l-amino acid with its d-enantiomer preserved the ability of the dipeptide to self-organize into nanotubes, as shown by single-crystal XRD analysis, whereby the pattern of electrostatic and hydrogen bonding interactions of the backbone was unaltered. The effect of heterochirality was manifested in subtle changes in the positioning of the aromatic side chains, which resulted in weaker intermolecular interactions between nanotubes. As a result, d-Phe-l-Phe self-organized into homogeneous nanofibrils with a diameter of 4 nm, corresponding to two layers of peptides around a water channel, and yielded a transparent hydrogel. In contrast with homochiral Phe-Phe stereoisomer, it formed stable hydrogels thermoreversibly. d-Phe-l-Phe displayed no amyloid toxicity in cell cultures with fibroblast cells proliferating in high numbers and viability on this biomaterial, marking it as a preferred substrate over tissue-culture plastic. Halogenation also enabled the tailoring of d-Phe-l-Phe self-organization. Fluorination allowed analogous supramolecular packing as confirmed by XRD, thus nanotube formation, and gave intermediate levels of bundling. In contrast, iodination was the most effective strategy to augment the stability of the resulting hydrogel, although at the expense of optical transparency and biocompatibility. Interestingly, iodine presence hindered the supramolecular packing into nanotubes, resulting instead into amphipathic layers of stacked peptides without the occurrence of halogen bonding. By unravelling fine details to control these materials at the meso- A nd macro-scale, this study significantly advanced our understanding of these systems

Imaging of SNR IC443 and W44 with the Sardinia Radio Telescope at 1.5 GHz and 7 GHz

Observations of supernova remnants (SNRs) are a powerful tool for investigating the later stages of stellar evolution, the properties of the ambient interstellar medium, and the physics of particle acceleration and shocks. For a fraction of SNRs, multi-wavelength coverage from radio to ultra high-energies has been provided, constraining their contributions to the production of Galactic cosmic rays. Although radio emission is the most common identifier of SNRs and a prime probe for refining models, high-resolution images at frequencies above 5 GHz are surprisingly lacking, even for bright and well-known SNRs such as IC443 and W44. In the frameworks of the Astronomical Validation and Early Science Program with the 64-m single-dish Sardinia Radio Telescope, we provided, for the first time, single-dish deep imaging at 7 GHz of the IC443 and W44 complexes coupled with spatially-resolved spectra in the 1.5-7 GHz frequency range. Our images were obtained through on-the-fly mapping techniques, providing antenna beam oversampling and resulting in accurate continuum flux density measurements. The integrated flux densities associated with IC443 are S_1.5GHz = 134 +/- 4 Jy and S_7GHz = 67 +/- 3 Jy. For W44, we measured total flux densities of S_1.5GHz = 214 +/- 6 Jy and S_7GHz = 94 +/- 4 Jy. Spectral index maps provide evidence of a wide physical parameter scatter among different SNR regions: a flat spectrum is observed from the brightest SNR regions at the shock, while steeper spectral indices (up to 0.7) are observed in fainter cooling regions, disentangling in this way different populations and spectra of radio/gamma-ray-emitting electrons in these SNRs.Comment: 13 pages, 9 figures, accepted for publication to MNRAS on 18 May 201

Sardinia Radio Telescope wide-band spectral-polarimetric observations of the galaxy cluster 3C 129

We present new observations of the galaxy cluster 3C 129 obtained with the Sardinia Radio Telescope in the frequency range 6000-7200 MHz, with the aim to image the large-angular-scale emission at high-frequency of the radio sources located in this cluster of galaxies. The data were acquired using the recently-commissioned ROACH2-based backend to produce full-Stokes image cubes of an area of 1 deg x 1 deg centered on the radio source 3C 129. We modeled and deconvolved the telescope beam pattern from the data. We also measured the instrumental polarization beam patterns to correct the polarization images for off-axis instrumental polarization. Total intensity images at an angular resolution of 2.9 arcmin were obtained for the tailed radio galaxy 3C 129 and for 13 more sources in the field, including 3C 129.1 at the galaxy cluster center. These data were used, in combination with literature data at lower frequencies, to derive the variation of the synchrotron spectrum of 3C 129 along the tail of the radio source. If the magnetic field is at the equipartition value, we showed that the lifetimes of radiating electrons result in a radiative age for 3C 129 of t_syn = 267 +/- 26 Myrs. Assuming a linear projected length of 488 kpc for the tail, we deduced that 3C 129 is moving supersonically with a Mach number of M=v_gal/c_s=1.47. Linearly polarized emission was clearly detected for both 3C 129 and 3C 129.1. The linear polarization measured for 3C 129 reaches levels as high as 70% in the faintest region of the source where the magnetic field is aligned with the direction of the tail.Comment: 19 pages, 17 figures, accepted for publication in MNRA

'I-I' and 'I-me' : Transposing Buber's interpersonal attitudes to the intrapersonal plane

Hermans' polyphonic model of the self proposes that dialogical relationships can be established between multiple I-positions1 (e.g., Hermans, 2001a). There have been few attempts, however, to explicitly characterize the forms that these intrapersonal relationships may take. Drawing on Buber's (1958) distinction between the 'I-Thou' and 'I-It' attitude, it is proposed that intrapersonal relationships can take one of two forms: an 'I-I' form, in which one I-position encounters and confirms another I-position in its uniqueness and wholeness; and an 'I-Me' form, in which one I-position experiences another I-position in a detached and objectifying way. This article argues that this I-Me form of intrapersonal relating is associated with psychological distress, and that this is so for a number of reasons: Most notably, because an individual who objectifies and subjugates certain I-position cannot reconnect with more central I-positions when dominance reversal (Hermans, 2001a) takes place. On this basis, it is suggested that a key role of the therapeutic process is to help clients become more able to experience moments of I-I intrapersonal encounter, and it is argued that this requires the therapist to confirm the client both as a whole and in terms of each of his or her different voices