Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model

Folding of Ubiquitin (Ub), a functionally important protein found in eukaryotic organisms, is investigated at low and neutral pH at different temperatures using simulations of the coarse-grained self-organized-polymer model with side chains (SOP-SC). The melting temperatures (T-m's), identified with the peaks in the heat capacity curves, decrease as pH decreases, in qualitative agreement with experiments. The calculated radius of gyration, showing dramatic variations with pH, is in excellent agreement with scattering experiments. At T-m Ub folds in a two-state manner at low and neutral pH. Clustering analysis of the conformations sampled in equilibrium folding trajectories at T-m with multiple transitions between the folded and unfolded states, shows a network of metastable states connecting the native and unfolded states. At low and neutral pH, Ub folds with high probability through a preferred set of conformations resulting in a pH-dependent dominant folding pathway. Folding kinetics reveal that Ub assembly at low pH occurs by multiple pathways involving a combination of nucleation-collapse and diffusion collision mechanism. The mechanism by which Ub folds is dictated by the stability of the key secondary structural elements responsible for establishing long-range contacts and collapse of Ub. Nucleation collapse mechanism holds if the stability of these elements are marginal, as would be the case at elevated temperatures. If the lifetimes associated with these structured microdomains are on the order of hundreds of microseconds, then Ub folding follows the diffusion collision mechanism with intermediates, many of which coincide with those found in equilibrium. Folding at neutral pH is a sequential process with a populated intermediate resembling that sampled at equilibrium. The transition state structures, obtained using a P-fold analysis, are homogeneous and globular with most of the secondary and tertiary structures being native-like. Many of our findings for both the thermodynamics and kinetics of folding are not only in agreement with experiments but also provide missing details not resolvable in standard experiments. The key prediction that folding mechanism varies dramatically with pH is amenable to experimental tests.

Controlled Release of Salicylic Acid from Biodegradable Cross-Linked Polyesters

The purpose of this work was to develop a family of crosslinked poly(xylitol adipate salicylate)s with a wide range of tunable release properties for delivering pharmacologically active salicylic acid. The synthesis parameters and release conditions were varied to modulate polyester properties and to understand the mechanism of release. Varying release rates were obtained upon longer curing (35% in the noncured polymer to 10% in the cured polymer in 7 days). Differential salicylic acid loading led to the synthesis of polymers with variable cross-linking and the release could be tuned (100% release for the lowest loading to 30% in the highest loading). Controlled release was monitored by changing various factors, and the release profiles were dependent on the stoichiometric composition, pH, curing time, and presence of enzyme. The polymer released a combination of salicylic acid and disalicylic acid, and the released products were found to be nontoxic. Minimal hemolysis and platelet activation indicated good blood compatibility. These polymers qualify as ``bioactive'' and ``resorbable'' and can, therefore, find applications as immunomodulatory resorbable biomaterials with tunable release properties.

An enzyme-linked immuno focus assay for rapid detection and enumeration, and a newborn mouse model for human non-polio enteroviruses associated with acute diarrhea

We have recently reported significant association of non-polio enteroviruses (NPEVs) with acute and persistent diarrhea (18-21% of total diarrheal cases), and non-diarrheal Increased Frequency of Bowel Movements (IFoBM-ND) (about 29% of the NPEV infections) in children and that the NPEV-associated diarrhea was as significant as rotavirus diarrhea. However, their diarrhea-causing potential is yet to be demonstrated in an animal model system. Since the determination of virus titers by the traditional plaque assay takes 4-7 days, there is a need for development of a rapid method for virus titer determination to facilitate active clinical research on enterovirus-associated diarrhea. The goal of this study is to develop a cell-based rapid detection and enumeration method and to demonstrate the diarrhea-inducing potential of purified and characterized non-polio enteroviruses, which were isolated from diarrheic children. Here we describe generation of monoclonal and polyclonal antibodies against purified strains belonging to different serotypes, and development of an enzyme-linked immuno focus assay (ELIFA) for detection and enumeration of live NPEV particles in clinical and purified virus samples, and a newborn mouse model for NPEV diarrhea. Plaque-purified NPVEs, belonging to different serotypes, isolated from children with diarrhea, were grown in cell culture and purified by isopycnic CsCl density gradient centrifugation. By ELIFA, NPEVs could be detected and enumerated within 12 h post-infection. Our results demonstrated that Coxsackievirus B1 (CVB1) and CVB5 strains, isolated from diarrheic children, induced severe diarrhea in orally-inoculated 9-12 day-old mouse pups, fulfilling Koch's postulates. The methods described here would facilitate studies on NPEV-associated gastrointestinal disease. (C) 2015 Elsevier B.V. All rights reserved.

Cyclic Cationic Peptides Containing Sugar Amino Acids Selectively Distinguishes and Inhibits Maturation of Pre-miRNAs of the Same Family

The discovery of microRNAs (miRNAs) has added a new dimension to the gene regulatory networks, making aberrantly expressed miRNAs as therapeutically important targets. Small molecules that can selectively target and modulate miRNA levels can thus serve as lead structures. Cationic cyclic peptides containing sugar amino acids represent a new class of small molecules that can target miRNA selectively. Upon treatment of these small molecules in breast cancer cell line, we profiled 96 therapeutically important miRNAs associated with cancer and observed that these peptides can selectively target paralogous miRNAs of the same seed family. This selective inhibition is of prime significance in cases when miRNAs of the same family have tissue-specific expression and perform different functions. During these conditions, targeting an entire miRNA family could lead to undesired adverse effects. The selective targeting is attributable to the difference in the three-dimensional structures of precursor miRNAs. Hence, the core structure of these peptides can be used as a scaffold for designing more potent inhibitors of miRNA maturation and hence function.

Relative stabilities of condensed face sharing mono- and di-carboranes: CB20H18 and C2B19H18+

The relative energies of triangular face sharing condensed macro polyhedral carboranes: CB20H18 and C2B19H18+ derived from mono- and di-substitution of carbons in (4) B21H18- is calculated at B3LYP/6-31G* level. The relative energies, H center dot center dot center dot H non-bonding distances, NICS values, topological charge analysis and orbital overlap compatibility connotes the face sharing condensed macro polyhedral mono-carboranes, 8 (4-CB20H18) to be the lowest energy isomer. The di-carba- derivative, (36) 4,4'a-C2B19H18+ with carbons substituted in a different B-12 cage in (4) B21H18- in anti-fashion is the most stable isomer among 28 possibilities. This structure has less non-bonding H center dot center dot center dot H interaction and is in agreement with orbital-overlap compatibility, and these two have the pivotal role in deciding the stability of these clusters. An estimate of the inherent stability of these carboranes is made using near-isodesmic equations which show that CB20H18 (8) is in the realm of the possible. (C) 2015 Elsevier B.V. All rights reserved.

Deviated linear cyclic pursuit

This paper analyses deviated linear cyclic pursuit in which an agent pursues its leader with an angle of deviation in both the continuous- and discrete-time domains, while admitting heterogeneous gains and deviations for the agents. Sufficient conditions for the stability of such systems, in both the domains, are presented in this paper along with the derivation of the reachable set, which is a set of points where the agents may converge asymptotically. The stability conditions are derived based on Gershgorin's theorem. Simulations validating the theoretical results presented in this paper are provided.

Impossibilità di pensare Dio non esistente : il Proslogion di Anselmo d'Aosta come applicazione implicita dei moderni procedimenti di logica aletica

Resumen: La vera intenzione teologica di Anselmo d’Aosta nello scrivere il Proslogion e il vero significato del suo celebre unum argumentum vanno visti nella funzione che la ragione svolge necessariamente all’interno della vita di fede del cristiano. Anselmo, come Tommaso d’Aquino, non sostiene che l’esistenza di Dio sia un “articulus fidei” ma piuttosto uno dei “praeambula fidei”. La ragione naturale ha la certezza che Dio esiste, ancora prima della dimostrazione metafisica, e questo non fa che confermare l’assurdità di pensare che non esista il fondamento reale di tutte le cose esistenti.

La distruzione delle statue di Pausania nella Sparta tardoantica (Lib. Ep. 1518)

Abstract: The late antique destruction of two bronze statues of Pausanias - the Spartan general responsible for the Greek victory at the Battle of Plataea (479 BC) - housed in the temple of Athena Chalkioikos in Sparta (Lib. Ep. 1518), has been interpreted as one of the few cases of a violent conflict between pagan and Christian population in Greece. Nevertheless the sources suggest that late antique Sparta was a bastion of Hellenic paganism and give a picture of a small and quiet town ruled by a pagan educated élite, where pagans like Libanius wanted to live. Since there is no evidence of a violent conflict between pagans and Christians in Sparta, and Libanius confirms that in 365 AD all the temples and cult statues were still in place, this paper addresses the issue from a different point of view and offers a new contribution to the history of Sparta in Late Antiquity. By using literary, archaeological and epigraphic evidence the paper explores: 1) the relationship between Roman administration and Spartan élite in the IVth century AD; 2) the historical memory of Pausanias in Late Antiquity. It will be emphasized that the obscure burning of the two statues helped to remove from Sparta the memory of Pausanias - a controversial figure, misrepresented in Late Antiquity and connected to the ancient staseis in Laconia - in order to promote a positive image of Sparta as a city without conflicts and ruled by the political system of Lycurgus (eunomia). As documented by local inscriptions in praise of late Roman governors, the mythical lawgiver Lycurgus was the paradigm of the imperial governors who rebuilded the town in the IVth cent. AD. It can be assumed that while Rome, Constantinople, Antioch and Athens were troubled by political and religious violence or by seditions between different factions, Sparta aimed to revive its traditional model of civic order in the new historical context of Late Antiquity.

On The Cyclic Bending Behaviour Of A Hard Coating On A Ductile Substrate With Periodic Surface Hardened Regions

A cyclic bending experiment is designed to investigate the interface fracture behaviour of a hard chromium coating on a ductile substrate with periodic surface hardened regions. The unique deflection pattern of the vertical cracks after they run through the coating and impinge at the interface is revealed experimentally. A simple double-layer elastic beam model is adopted to investigate the interfacial shear stresses analytically. A FE model is employed to compute the stresses of the tri-phase structure under a single round of bending, and to investigate the effect of the loading conditions on the deflection pattern of the vertical cracks at the interface. (C) 2008 Elsevier Ltd. All rights reserved.

Stability Of Adhesion Clusters And Cell Reorientation Under Lateral Cyclic Tension

This work is motivated by experimental observations that cells on stretched substrate exhibit different responses to static and dynamic loads. A model of focal adhesion that can consider the mechanics of stress fiber, adhesion bonds, and substrate was developed at the molecular level by treating the focal adhesion as an adhesion cluster. The stability of the cluster under dynamic load was studied by applying cyclic external strain on the substrate. We show that a threshold value of external strain amplitude exists beyond which the adhesion cluster disrupts quickly. In addition, our results show that the adhesion cluster is prone to losing stability under high-frequency loading, because the receptors and ligands cannot get enough contact time to form bonds due to the high-speed deformation of the substrate. At the same time, the viscoelastic stress fiber becomes rigid at high frequency, which leads to significant deformation of the bonds. Furthermore, we find that the stiffness and relaxation time of stress fibers play important roles in the stability of the adhesion cluster. The essence of this work is to connect the dynamics of the adhesion bonds (molecular level) with the cell's behavior during reorientation (cell level) through the mechanics of stress fiber. The predictions of the cluster model are consistent with experimental observations.

Centrifuge modeling of suction bucket foundations for platforms under ice-sheet-induced cyclic lateral loadings

This paper presents the results of a series of centrifuge model tests performed to study the behavior of suction bucket foundations for a tension leg platform in the Bohai Bay, China. The target lateral loadings were from ice-sheet-induced structural vibrations at a frequency of 0.8-1.0 Hz. The results indicate that excess pore water pressures reach the highest values within a depth of 1.0-1.5 in below the mud line. The pore pressures and the induced settlement and lateral displacement increase with the amplitude of the cyclic loading. Two failure modes were observed: liquefaction in early excitations and settlement-induced problems after long-term excitations. (c) 2006 Elsevier Ltd. All rights reserved.

Evaluación de la eficacia de la técnica de floating system para la producción de radicchio rosso var. di Verona en condiciones controladas

La técnica de producción en Floating system constituye una alternativa económica y veloz de producción en hidroponia. Este sistema permite obtener hojas de vegetales de pequeño tamaño “Baby leaf” listas para consumir (IV Gama), cuyo consumo a nivel mundial muestra una tendencia creciente. Dicha técnica no se encuentra aún muy difundida para la producción de radicchio rosso. El objetivo de este trabajo fue evaluar el efecto del tamaño de celda, del substrato y de la técnica de floating system sobre la producción de radicchio. Los ensayos se realizaron en cámara a 25 ºC con un fotoperíodo de 16 hs de luz y 8 de oscuridad y con una intensidad de luz de 10 000 Lux. Se utilizó un diseño experimental factorial totalmente aleatorizado, con 5 repeticiones y 3 factores, cuyos niveles fueron: 1) Tamaño de celda, (T), con 3 niveles: grande, mediano y pequeño, 2) Técnica de producción, (F), con 2 niveles: floating system y sistema convencional, 3) Sustrato, (S), con 2 niveles: vermiculita y mezcla. Se analizaron las siguientes variables: 1) peso fresco, 2) peso seco, 3) largo de planta, 4) número de hojas y 5) área foliar. Los resultados obtenidos resultan alentadores respecto del empleo de la técnica de floating system. Para la obtención de plántulas con calidad de IV Gama resulta más conveniente el empleo de celdas de 80 cm3 y sustrato mezcla.