Biosynthesis, structure, and biological activities of envelope protein gp65 of murine coronavirus.

We have previously shown that gp65 (E3) is a virion structural protein which varies widely in quantity among different strains of mouse hepatitis virus (MHV). In this study, the biosynthetic pathway and possible biological activities of this protein were examined. The glycosylation of gp65 in virus-infected cells was inhibited by tunicamycin but not by monensin, suggesting that it contains an N-glycosidic linkage. Glycosylation is cotranslational and appears to be complete before the glycoprotein reaches the Golgi complex. Pulse-chase experiments showed that this protein decreased in size after 30 min of chase, suggesting that the carbohydrate chains of gp65 undergo trimming during its transport across the Golgi. This interpretation is supported by the endoglycosidase treatment of gp65, which showed that the peptide backbone of gp65 did not decrease in size after pulse-chase periods. This maturation pathway is distinct from that of the E1 or E2 glycoproteins. Partial endoglycosidase treatment indicated that gp65 contains 9 to 10 carbohydrate side chains; thus, almost all of the potential glycosylation sites of gp65 were glycosylated. In vitro translation studies coupled with protease digestion suggest that gp65 is an integral membrane protein. The presence of gp65 in the virion is correlated with the presence of an acetylesterase activity. No hemagglutinin activity was detected

Competing interactions in two dimensional Coulomb systems: Surface charge heterogeneities in co-assembled cationic-anionic incompatible mixtures

A binary mixture of oppositely charged components confined to a plane such as cationic and anionic lipid bilayers may exhibit local segregation. The relative strength of the net short range interactions, which favors macroscopic segregation, and the long range electrostatic interactions, which favors mixing, determines the length scale of the finite size or microphase segregation. The free energy of the system can be examined analytically in two separate regimes, when considering small density fluctuations at high temperatures, and when considering the periodic ordering of the system at low temperatures (F. J. Solis and M. Olvera de la Cruz, J. Chem. Phys. 122, 054905 (2000)). A simple Molecular Dynamics simulation of oppositely charged monomers, interacting with a short range Lennard Jones potential and confined to a two dimensional plane, is examined at different strengths of short and long range interactions. The system exhibits well-defined domains that can be characterized by their periodic length-scale as well as the orientational ordering of their interfaces. By adding salt, the ordering of the domains disappears and the mixture macroscopically phase segregates in agreement with analytical predictions.Comment: 8 pages, 5 figures, accepted for publication in J. Chem. Phys, Figure 1 include

Ion condensation on charged patterned surfaces

We study ion condensation onto a patterned surface of alternating charges. The competition between self-energy and ion-surface interactions leads to the formation of ionic crystalline structures at low temperatures. We consider different arrangements of underlying ionic crystals, including single ion adsorption, as well as the formation of dipoles at the interface between charged domains. Molecular dynamic simulation illustrates existence of single and mixed phases. Our results contribute to understanding pattern recognition, and molecular separation and synthesis near patterned surfaces.Comment: 3 figure

Multiple effects of CDK4/6 inhibition in cancer: From cell cycle arrest to immunomodulation

Dysregulation of the cell cycle is a hallmark of cancer that leads to aberrant cellular proliferation. CDK4/6 are cyclin-dependent kinases activated in response to proliferative signaling, which induce RB hyper-phosphorylation and hence activation of E2F transcription factors, thus promoting cell cycle progression through the S phase. Pharmacologic inhibition of CDK4/6 by palbociclib, ribociclib, or abemaciclib has been showing promising activity in multiple cancers with the best results achieved in combination with other agents. Indeed, CDK4/6 inhibitors are currently approved in combination with endocrine therapy for the treatment of estrogen receptor-positive, human epidermal growth factor receptor 2-negative advanced or metastatic breast cancer. Moreover, a number of clinical trials are currently underway to test the efficacy of combining CDK4/6 inhibitors with different drugs not only in breast but also in other types of cancer. Beyond the inhibition of cell proliferation, CDK4/6 inhibitors have recently revealed new effects on cancer cells and on tumor microenvironment. In particular, it has been reported that these agents induce a senescent-like phenotype, impact on cell metabolism and exert both immunomodulatory and immunogenic effects. Here we describe recent data on the anti-tumor effects of CDK4/6 inhibitors as single agents or in combined therapies, focusing in particular on their metabolic and immunomodulatory activities

Complexity of qualitative timeline-based planning

The timeline-based approach to automated planning was originally developed in the context of space missions. In this approach, problem domains are expressed as systems consisting of independent but interacting components whose behaviors over time, the timelines, are governed by a set of temporal constraints, called synchronization rules. Although timeline-based system descriptions have been successfully used in practice for decades, the research on the theoretical aspects only started recently. In the last few years, some interesting results have been shown concerning both its expressive power and the computational complexity of the related planning problem. In particular, the general problem has been proved to be EXPSPACE-complete. Given the applicability of the approach in many practical scenarios, it is thus natural to ask whether computationally simpler but still expressive fragments can be identified. In this paper, we study the timeline-based planning problem with the restriction that only qualitative synchronization rules, i.e., rules without explicit time bounds in the constraints, are allowed. We show that the problem becomes PSPACE-complete

Non-monotonic swelling of surface grafted hydrogels induced by pH and/or salt concentration

We use a molecular theory to study the thermodynamics of a weak-polyacid hydrogel film that is chemically grafted to a solid surface. We investigate the response of the material to changes in the pH and salt concentration of the buffer solution. Our results show that the pH-triggered swelling of the hydrogel film has a non-monotonic dependence on the acidity of the bath solution. At most salt concentrations, the thickness of the hydrogel film presents a maximum when the pH of the solution is increased from acidic values. The quantitative details of such swelling behavior, which is not observed when the film is physically deposited on the surface, depend on the molecular architecture of the polymer network. This swelling-deswelling transition is the consequence of the complex interplay between the chemical free energy (acid-base equilibrium), the electrostatic repulsions between charged monomers, which are both modulated by the absorption of ions, and the ability of the polymer network to regulate charge and control its volume (molecular organization). In the absence of such competition, for example, for high salt concentrations, the film swells monotonically with increasing pH. A deswelling-swelling transition is similarly predicted as a function of the salt concentration at intermediate pH values. This reentrant behavior, which is due to the coupling between charge regulation and the two opposing effects triggered by salt concentration (screening electrostatic interactions and charging/discharging the acid groups), is similar to that found in end-grafted weak polyelectrolyte layers. Understanding how to control the response of the material to different stimuli, in terms of its molecular structure and local chemical composition, can help the targeted design of applications with extended functionality. We describe the response of the material to an applied pressure and an electric potential. We present profiles that outline the local chemical composition of the hydrogel, which can be useful information when designing applications that pursue or require the absorption of biomolecules or pH-sensitive molecules within different regions of the film.Fil: Longo, Gabriel Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico la Plata. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas; Argentina. Northwestern University. Department of Biomedical Engineering; Estados Unidos. Northwestern University. Chemistry of Life Processes Institute; Estados UnidosFil: Olvera de la Cruz, Monica. Northwestern University; Estados UnidosFil: Szleifer, Igal. Northwestern University; Estados Unido

Thesaurus: un database per il patrimonio culturale sommerso

Thesaurus Project aims at promoting the knowledge of the underwater cultural heritage, ancient and modern, through the application of several typologies of tools: underwater autonomous vehicles, which will be able to explore the sea bottom in teams communicating with each other; a database, which will be useful to store and manage all the information referring to archaeological or historical objects, shipwrecks and sites. This paper aims to explain the logic structure of the database indicating the particular needs of the research, the different typologies of items which have to be managed (archaeological and historical objects; ancient, medieval or modern shipwrecks; underwater sites; written or figurative sources, etc.), the relation with other similar databases and projects. The main task of this part of Thesaurus is to plan and organize an IT system, which will allow archaeologists to describe information in detail, in order to make an efficient managing and retrieving data system available

Antiproliferative Activity Predictor: A New Reliable In Silico Tool for Drug Response Prediction against NCI60 Panel

In vitro antiproliferative assays still represent one of the most important tools in the anticancer drug discovery field, especially to gain insights into the mechanisms of action of anticancer small molecules. The NCI-DTP (National Cancer Institute Developmental Therapeutics Program) undoubtedly represents the most famous project aimed at rapidly testing thousands of compounds against multiple tumor cell lines (NCI60). The large amount of biological data stored in the National Cancer Institute (NCI) database and many other databases has led researchers in the fields of computational biology and medicinal chemistry to develop tools to predict the anticancer properties of new agents in advance. In this work, based on the available antiproliferative data collected by the NCI and the manipulation of molecular descriptors, we propose the new in silico Antiproliferative Activity Predictor (AAP) tool to calculate the GI50 values of input structures against the NCI60 panel. This ligand-based protocol, validated by both internal and external sets of structures, has proven to be highly reliable and robust. The obtained GI50 values of a test set of 99 structures present an error of less than ±1 unit. The AAP is more powerful for GI50 calculation in the range of 4–6, showing that the results strictly correlate with the experimental data. The encouraging results were further supported by the examination of an in-house database of curcumin analogues that have already been studied as antiproliferative agents. The AAP tool identified several potentially active compounds, and a subsequent evaluation of a set of molecules selected by the NCI for the one-dose/five-dose antiproliferative assays confirmed the great potential of our protocol for the development of new anticancer small molecules. The integration of the AAP tool in the free web service DRUDIT provides an interesting device for the discovery and/or optimization of anticancer drugs to the medicinal chemistry community. The training set will be updated with new NCI-tested compounds to cover more chemical spaces, activities, and cell lines. Currently, the same protocol is being developed for predicting the TGI (total growth inhibition) and LC50 (median lethal concentration) parameters to estimate toxicity profiles of small molecules