Unifying thermodynamic and kinetic descriptions of single-molecule processes: RNA unfolding under tension

We use mesoscopic non-equilibrium thermodynamics theory to describe RNA unfolding under tension. The theory introduces reaction coordinates, characterizing a continuum of states for each bond in the molecule. The unfolding considered is so slow that one can assume local equilibrium in the space of the reaction coordinates. In the quasi-stationary limit of high sequential barriers, our theory yields the master equation of a recently proposed sequential-step model. Non-linear switching kinetics is found between open and closed states. Our theory unifies the thermodynamic and kinetic descriptions and offers a systematic procedure to characterize the dynamics of the unfolding processComment: 13 pages, 3 figure

Regulation of Antigen-Experienced T Cells: Lessons from the Quintessential Memory Marker CD44

Despite the widespread use of the cell-surface receptor CD44 as a marker for antigen (Ag)-experienced, effector and memory T cells, surprisingly little is known regarding its function on these cells. The best-established function of CD44 is the regulation of cell adhesion and migration. As such, the interactions of CD44, primarily with its major ligand, the extracellular matrix (ECM) component hyaluronic acid (HA), can be crucial for the recruitment and function of effector and memory T cells into/within inflamed tissues. However, little is known about the signaling events following engagement of CD44 on T cells and how cooperative interactions of CD44 with other surface receptors affect T cell responses. Recent evidence suggests that the CD44 signaling pathway(s) may be shared with those of other adhesion receptors, and that these provide contextual signals at different anatomical sites to ensure the correct T cell effector responses. Furthermore, CD44 ligation may augment T cell activation after Ag encounter and promote T cell survival, as well as contribute to regulation of the contraction phase of an immune response and the maintenance of tolerance. Once the memory phase is established, CD44 may have a role in ensuring the functional fitness of memory T cells. Thus, the summation of potential signals after CD44 ligation on T cells highlights that migration and adhesion to the ECM can critically impact the development and homeostasis of memory T cells, and may differentially affect subsets of T cells. These aspects of CD44 biology on T cells and how they might be modulated for translational purposes are discussed

Effect of Cytisus multiflorus in the control of Type-2 Diabetes

Medicinal plants display diverse pharmacological activities with marked therapeutic effects. Type-2 diabetes (T2D) remains a major health problem among industrialized countries, therefore the investigation of formulas to prevent or attenuate the metabolic syndrome, including new therapeutic agents. Currently the interest of medicinal plants is increasing. Portuguese native flora includes several plants known for their hypoglycemic properties. The aim of this work was to study the pharmacological effect of Cytisus multiflorus, one plant from the Portuguese flora traditionally used as an ethnopharmacological agent in diabetes control

Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding

Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as the template. The ribosome is a molecular motor that utilizes the template mRNA strand also as the track. Thus, in each step the ribosome moves forward by one codon and, simultaneously, elongates the protein by one amino acid. We present a theoretical model that captures most of the main steps in the mechano-chemical cycle of a ribosome. The stochastic movement of the ribosome consists of an alternating sequence of pause and translocation; the sum of the durations of a pause and the following translocation is the time of dwell of the ribosome at the corresponding codon. We derive the analytical expression for the distribution of the dwell times of a ribosome in our model. Whereever experimental data are available, our theoretical predictions are consistent with those results. We suggest appropriate experiments to test the new predictions of our model, particularly, the effects of the quality control mechanism of the ribosome and that of their crowding on the mRNA track.Comment: This is an author-created, un-copyedited version of an article accepted for publication in Physical Biology. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The definitive publisher authenticated version is available online at DOI:10.1088/1478-3975/8/2/02600

Acoustic-like dynamics of amorphous drugs in the THz regime

The high frequency dynamics of Indomethacin and Celecoxib glasses has been investigated by inelastic x-ray scattering, accessing a momentum-energy region still unexplored in amorphous pharmaceuticals. We find evidence of phonon-like acoustic dynamics, and determine the THz behavior of sound velocity and acoustic attenuation. Connections with ordinary sound propagation are discussed, along with the relation between fast and slow degrees of freedom as represented by non-ergodicity factor and kinetic fragility, respectively

Probing protein sequences as sources for encrypted antimicrobial peptides

Starting from the premise that a wealth of potentially biologically active peptides may lurk within proteins, we describe here a methodology to identify putative antimicrobial peptides encrypted in protein sequences. Candidate peptides were identified using a new screening procedure based on physicochemical criteria to reveal matching peptides within protein databases. Fifteen such peptides, along with a range of natural antimicrobial peptides, were examined using DSC and CD to characterize their interaction with phospholipid membranes. Principal component analysis of DSC data shows that the investigated peptides group according to their effects on the main phase transition of phospholipid vesicles, and that these effects correlate both to antimicrobial activity and to the changes in peptide secondary structure. Consequently, we have been able to identify novel antimicrobial peptides from larger proteins not hitherto associated with such activity, mimicking endogenous and/or exogenous microorganism enzymatic processing of parent proteins to smaller bioactive molecules. A biotechnological application for this methodology is explored. Soybean (Glycine max) plants, transformed to include a putative antimicrobial protein fragment encoded in its own genome were tested for tolerance against Phakopsora pachyrhizi, the causative agent of the Asian soybean rust. This procedure may represent an inventive alternative to the transgenic technology, since the genetic material to be used belongs to the host organism and not to exogenous sources

Structure of Polyelectrolytes in Poor Solvent

We present simulations on charged polymers in poor solvent. First we investigate in detail the dilute concentration range with and without imposed extension constraints. The resulting necklace polymer conformations are analyzed in detail. We find strong fluctuations in the number of pearls and their sizes leading only to small signatures in the form factor and the force-extension relation. The scaling of the peak in the structure factor with the monomer density shows a pertinent different behavior from good solvent chains.Comment: 7 pages, 5 figures. submitted to EP

Electronic and phononic properties of the chalcopyrite CuGaS2

The availability of ab initio electronic calculations and the concomitant techniques for deriving the corresponding lattice dynamics have been profusely used for calculating thermodynamic and vibrational properties of semiconductors, as well as their dependence on isotopic masses. The latter have been compared with experimental data for elemental and binary semiconductors with different isotopic compositions. Here we present theoretical and experimental data for several vibronic and thermodynamic properties of CuGa2, a canonical ternary semiconductor of the chalcopyrite family. Among these properties are the lattice parameters, the phonon dispersion relations and densities of states (projected on the Cu, Ga, and S constituents), the specific heat and the volume thermal expansion coefficient. The calculations were performed with the ABINIT and VASP codes within the LDA approximation for exchange and correlation and the results are compared with data obtained on samples with the natural isotope composition for Cu, Ga and S, as well as for isotope enriched samples.Comment: 9 pages, 8 Figures, submitted to Phys. Rev

Advanced tools and techniques to add value to soil stabilization practice

The aim of this paper is to demonstrate the advanced tools and techniques used for adding value to the soil stabilization practice. The tools presented involve advanced laboratory tests and modeling using codes and soft computing to evaluate the mechanical behavior of stabilized soils with cement, ranging from short-term to long-term behavior. More precisely, these tools are able to: 1. Predict the mechanical behavior of the stabilized soils over time from data obtained in the early ages saving time in laboratory tests; 2. Predict the mechanical behavior of the stabilized soils over time based on basic parameters of soil type and binder using historical accurate data, avoiding mechanical laboratory tests. 3. Incorporate the serviceability limit state concept in a novel proposal to estimate the design modulus in function of the uniaxial compressive strength and the strain level, making more economic and sustainable geotechnical solutions.This work was supported by FCT—‘‘Fundação para a Ciência e a Tecnologia’’, within ISISE, project UID/ECI/04029/2013 and through the post doctoral Grant fellowship with reference SFRH/BPD/94792/2013. This work was also partly financed by FEDER funds through the Competitivity Factors Operational Programme—COMPETE and by national funds through FCT within the scope of the project POCI-01-0145-FEDER-007633.info:eu-repo/semantics/publishedVersio