On the electronic nature of low-barrier hydrogen bonds in enzymatic reactions

The electronic nature of low-barrier hydrogen bonds (LBHBs) in enzymatic reactions is discussed based on combined low temperature neutron and x-ray diffraction experiments and on high level ab initio calculations by using the model substrate benzoylacetone. This molecule has a LBHB, as the intramolecular hydrogen bond is described by a double-well potential with a small barrier for hydrogen transfer. From an “atoms in molecules” analysis of the electron density, it is found that the hydrogen atom is stabilized by covalent bonds to both oxygens. Large atomic partial charges on the hydrogen-bonded atoms are found experimentally and theoretically. Therefore, the hydrogen bond gains stabilization from both covalency and from the normal electrostatic interactions found for long, weak hydrogen bonds. Based on comparisons with other systems having short-strong hydrogen bonds or LBHBs, it is proposed that all short-strong and LBHB systems possess similar electronic features of the hydrogen-bonded region, namely polar covalent bonds between the hydrogen atom and both heteroatoms in question.

Two Components of Actin-based Retrograde Flow in Sea Urchin Coelomocytes

Sea urchin coelomocytes represent an excellent experimental model system for studying retrograde flow. Their extreme flatness allows for excellent microscopic visualization. Their discoid shape provides a radially symmetric geometry, which simplifies analysis of the flow pattern. Finally, the nonmotile nature of the cells allows for the retrograde flow to be analyzed in the absence of cell translocation. In this study we have begun an analysis of the retrograde flow mechanism by characterizing its kinetic and structural properties. The supramolecular organization of actin and myosin II was investigated using light and electron microscopic methods. Light microscopic immunolocalization was performed with anti-actin and anti-sea urchin egg myosin II antibodies, whereas transmission electron microscopy was performed on platinum replicas of critical point-dried and rotary-shadowed cytoskeletons. Coelomocytes contain a dense cortical actin network, which feeds into an extensive array of radial bundles in the interior. These actin bundles terminate in a perinuclear region, which contains a ring of myosin II bipolar minifilaments. Retrograde flow was arrested either by interfering with actin polymerization or by inhibiting myosin II function, but the pathway by which the flow was blocked was different for the two kinds of inhibitory treatments. Inhibition of actin polymerization with cytochalasin D caused the actin cytoskeleton to separate from the cell margin and undergo a finite retrograde retraction. In contrast, inhibition of myosin II function either with the wide-spectrum protein kinase inhibitor staurosporine or the myosin light chain kinase–specific inhibitor KT5926 stopped flow in the cell center, whereas normal retrograde flow continued at the cell periphery. These differential results suggest that the mechanism of retrograde flow has two, spatially segregated components. We propose a “push–pull” mechanism in which actin polymerization drives flow at the cell periphery, whereas myosin II provides the tension on the actin cytoskeleton necessary for flow in the cell interior.

Nature knows best: An amazing reaction cascade is uncovered by design and discovery

The Daphniphyllum alkaloids are a group of highly complex polycyclic alkaloids. Examination of the structures if several members of this family of natural products led to a hypothesis about their mode of biosynthesis (depicted in Scheme SI). Based on this hypothetical biosynthetic pathway, a laboratory synthesis was designed that incorporated as a key transformation the novel one-pot transformation of dialdehyde 24 to pentacyclic unsaturated amine 25. This process turned out to be an exceptionally efficient way to construct the pentacyclic nucleus of the Daphniphyllum alkaloids. However, a purely fortuitous discovery, resulting from accidental use of methylamine rather than ammonia, led to a great improvement in the synthesis and suggests an even more attractive possible biosynthesis.

Fluorescence-based directed termination PCR: direct mutation characterization without sequencing

We describe a fluorescence-based directed termination PCR (fluorescent DT–PCR) that allows accurate determination of actual sequence changes without dideoxy DNA sequencing. This is achieved using near infrared dye-labeled primers and performing two PCR reactions under low and unbalanced dNTP concentrations. Visualization of resulting termination fragments is accomplished with a dual dye Li-cor DNA sequencer. As each DT–PCR reaction generates two sets of terminating fragments, a pair of complementary reactions with limiting dATP and dCTP collectively provide information on the entire sequence of a target DNA, allowing an accurate determination of any base change. Blind analysis of 78 mutants of the supF reporter gene using fluorescent DT–PCR not only correctly determined the nature and position of all types of substitution mutations in the supF gene, but also allowed rapid scanning of the signature sequences among identical mutations. The method provides simplicity in the generation of terminating fragments and 100% accuracy in mutation characterization. Fluorescent DT–PCR was successfully used to generate a UV-induced spectrum of mutations in the supF gene following replication on a single plate of human DNA repair-deficient cells. We anticipate that the automated DT–PCR method will serve as a cost-effective alternative to dideoxy sequencing in studies involving large-scale analysis for nucleotide sequence changes.

Interfacial activation-based molecular bioimprinting of lipolytic enzymes.

Interfacial activation-based molecular (bio)-imprinting (IAMI) has been developed to rationally improve the performance of lipolytic enzymes in nonaqueous environments. The strategy combinedly exploits (i) the known dramatic enhancement of the protein conformational rigidity in a water-restricted milieu and (ii) the reported conformational changes associated with the activation of these enzymes at lipid-water interfaces, which basically involves an increased substrate accessibility to the active site and/or an induction of a more competent catalytic machinery. Six model enzymes have been assayed in several model reactions in nonaqueous media. The results, rationalized in light of the present biochemical and structural knowledge, show that the IAMI approach represents a straightforward, versatile method to generate manageable, activated (kinetically trapped) forms of lipolytic enzymes, providing under optimal conditions nonaqueous rate enhancements of up to two orders of magnitude. It is also shown that imprintability of lipolytic enzymes depends not only on the nature of the enzyme but also on the "quality" of the interface used as the template.

New multivalent calixarene-based ligands for protein recognition and inhibition

One of the challenges that concerns chemistry is the design of molecules able to modulate protein-protein and protein-ligand interactions, since these are involved in many physiological and pathological processes. The interactions occurring between proteins and their natural counterparts can take place through reciprocal recognition of rather large surface areas, through recognition of single contact points and single residues, through inclusion of the substrates in specific, more or less deep binding sites. In many cases, the design of synthetic molecules able to interfere with the processes involving proteins can benefit from the possibility of exploiting the multivalent effect. Multivalency, widely spread in Nature, consists in the simultaneous formation between two entities (cell-cell, cell-protein, protein-protein) of multiple equivalent ligand-recognition site complexes. In this way the whole interaction results particularly strong and specific. Calixarenes furnish a very interesting scaffold for the preparation of multivalent ligands and in the last years calixarene-based ligands demonstrated their remarkable capability to recognize and inhibit or restore the activity of different proteins, with a high efficiency and selectivity in several recognition phenomena. The relevance and versatility of these ligands is due to the different exposition geometries of the binding units that can be explored exploiting the conformational properties of these macrocycles, the wide variety of functionalities that can be linked to their structure at different distances from the aromatic units and to their intrinsic multivalent nature. With the aim of creating new multivalent systems for protein targeting, the work reported in this thesis regards the synthesis and properties of glycocalix[n]arenes and guanidino calix[4]arenes for different purposes. Firstly, a new bolaamphiphile glycocalix[4]arene in 1,3-alternate geometry, bearing cellobiose, was synthesized for the preparation of targeted drug delivery systems based on liposomes. The formed stable mixed liposomes obtained by mixing the macrocycle with DOPC were shown to be able of exploiting the sugar units emerging from the lipid bilayer to agglutinate Concanavalin A, a lectin specific for glucose. Moreover, always thanks to the presence of the glycocalixarene in the layer, the same liposomes demonstrated through preliminary experiments to be uptaken by cancer cells overexpressing glucose receptors on their exterior surface more efficiently respect to simple DOPC liposomes lacking glucose units in their structure. Then a small library of glycocalix[n]arenes having different valency and geometry was prepared, for the creation of potentially active immunostimulants against Streptococcus pneumoniae, particularly the 19F serotype, one of the most virulent. These synthesized glycocalixarenes bearing β-N-acetylmannosamine as antigenic unit were compared with the natural polysaccharide on the binding to the specific anti-19F human polyclonal antibody, to verify their inhibition potency. Among all, the glycocalixarene based on the conformationally mobile calix[4]arene resulted the more efficient ligand, probably due its major possibility to explore the antibody surface and dispose the antigenic units in a proper arrangement for the interaction process. These results pointed out the importance of how the different multivalent presentation in space of the glycosyl units can influence the recognition phenomena. At last, NMR studies, using particularly 1H-15N HSQC experiments, were performed on selected glycocalix[6]arenes and guanidino calix[4]arenes blocked in the cone geometry, in order to better understand protein-ligand interactions. The glycosylated compounds were studied with Ralstonia solanacearum lectin, in order to better understand the nature of the carbohydrate‐lectin interactions in solution. The series of cationic calixarene was employed with three different acidic proteins: GB1, Fld and alpha synuclein. Particularly GB1 and Fld were observed to interact with all five cationic calix[4]arenes but showing different behaviours and affinities.

A new modularity measure for Fuzzy Community detection problems based on overlap and grouping functions

One of the main challenges of fuzzy community detection problems is to be able to measure the quality of a fuzzy partition. In this paper, we present an alternative way of measuring the quality of a fuzzy community detection output based on n-dimensional grouping and overlap functions. Moreover, the proposed modularity measure generalizes the classical Girvan–Newman (GN) modularity for crisp community detection problems and also for crisp overlapping community detection problems. Therefore, it can be used to compare partitions of different nature (i.e. those composed of classical, overlapping and fuzzy communities). Particularly, as is usually done with the GN modularity, the proposed measure may be used to identify the optimal number of communities to be obtained by any network clustering algorithm in a given network. We illustrate this usage by adapting in this way a well-known algorithm for fuzzy community detection problems, extending it to also deal with overlapping community detection problems and produce a ranking of the overlapping nodes. Some computational experiments show the feasibility of the proposed approach to modularity measures through n-dimensional overlap and grouping functions.

Through the Eyes of Visitors: Understanding the Contexts of the Visitor Photo Study at the Denver Museum of Nature & Science

This case study describes the analysis of the Visitor Photo Study, a study in which visitors to the Denver Museum of Nature & Science documented their visit through pictures. The origins, implementation, and findings of the Visitor Photo Study are considered within the contexts of the fields of Community-Based Research (Strand, Marullo, Cutforth, Stoecker, & Donohue, 2003b), Visual Studies (Marshall & Rossman, 2011; Pink, 2007), and Visitor Studies (Visitor Studies Association, 2012). This study considers the extent to which the principles and elements of each of these fields were present in the Visitor Photo Study, which elements were not fully realized or were missing from the study, and ways in which the Visitor Photo Study extends each of these fields. The value of this type of analysis and implications for museums, faculty, and students are also discussed.

The Use of Humor in Therapy : Research-Based Training Recommendations

Despite its essential and universal nature, humor has historically received limited attention from the behavioral sciences, particularly as compared to other affective experiences like anger and sadness. Some authors (e.g., Bell & Malhi, 2009; Provine, 2000a; Roeckelein, 2002) suggest that this is because researchers have traditionally failed to "take humor seriously" and, according to O'Connell (cited in Roeckelein, 2002), have too often pursued its study in a piecemeal manner lacking scientific rigor, resulting in "no comprehensive network of facts about the development and purposes of humor in human existence" (p. 1). Roeckelein (2002) found not a single mention of humor, laughter, wit, comedy, or theories relating to these topics in introductory psychology textbooks published between 1930 and 1996.While research interest in the area has grown, especially over the last decade, it remains an elusive and nebulous topic, more likely to be examined in specialty psychology texts (e.g., social psychology and child development) than general ones (Martin, 2007; Roeckelein, 2002). Organizations (e.g., The International Society for Humor Studies; The Association for the Advancement of Therapeutic Humor), journals (e.g., Humor: International Journal of Humor Research) and internet phenomena such as "The Humor Project" (www.humorproiect.com) have made great strides in integrating information about humor from discreet fields such as the arts and humanities, biological and social sciences, education, and business management. Still, the therapeutic potential of humor remains a relatively young subject of serious scientific inquiry (Marci, Moran, & Orr, 2004; Sala, Krupat, & Roter, 2002). While humor does make appearances in self-help books and publications addressing clinical applications, these sources are much ...

Snakes based tracking and texture analysis of microscopic images

Comunicación presentada en el VII Symposium Nacional de Reconocimiento de Formas y Análisis de Imágenes, SNRFAI, Barcelona, abril 1997.

Processing and Characterization of Nano-biocomposites Based on Mater-Bi® with Layered Silicates

The development of new nano-biocomposites has been one of the main research areas of interest in polymer science in recent years, since they can combine the intrinsic biodegradable nature of matrices with the ability to modify their properties by the addition of selected nano-reinforcements. In this work, the addition of mineral nanoclays (montmorillonites and sepiolites) to a commercial starch-based matrix is proposed. A complete study on their processing by melt-intercalation techniques and further evaluation of the main properties of nano-biocomposites has been carried out. The results reported show an important influence of the nano-biocomposites morphology on their final properties. In particular, the rheological and viscoelastic characteristics of these systems are very sensitive to the dispersion level of the nanofiller, but it is possible to assess that the material processing behaviour is not compromised by the presence of these nano-reinforcements. In general, both nanofillers had a positive influence in the materials final properties. Mechanical performance shows improvements in terms of elastic modulus, without important limitations in terms of ductility. Thermal properties are improved in terms of residual mass after degradation and low improvements are also observed in terms of oxygen barrier properties.

Effect of the surface chemical groups of activated carbons on their surface adsorptivity to aromatic adsorbates based on π-π interactions

Three activated carbons with different surface chemical groups were used to analyse the influence of these groups on their adsorption capacities towards aromatic-type molecules whose adsorption is based on π-π interactions with surface arene centres. The three activated carbons studied were a low-functionalized carbon (Merck), an oxygen-rich carbon obtained by HNO3 oxidation of Merck, and a nitrogen-rich carbon also prepared from Merck by mild HNO3 oxidation followed by treatment with a dicyanodiamide/dimethyl formamide mixture at 300 °C. The nature of the surface chemical groups of the three activated carbons was investigated by both physical and chemical techniques (TPD, XPS, Boehm analysis and pH potentiometric titration). A systematic study of the adsorptions of a series of analogous aromatic adsorbates on the three activated carbons was carried out to study the adsorption mechanisms. In all cases the adsorption mechanism is based on π-π interactions between the aromatic moiety of the adsorbates and the arene centres of the graphite sheets. The differences in the normalized adsorption capacities of the adsorbents for a set of adsorbates indicate that the π-donor or π-withdrawing character of the functional groups have a clear influence on the basicity of the arene centres.

A new boundary-based morphological model

Mathematical morphology addresses the problem of describing shapes in an n-dimensional space using the concepts of set theory. A series of standardized morphological operations are defined, and they are applied to the shapes to transform them using another shape called the structuring element. In an industrial environment, the process of manufacturing a piece is based on the manipulation of a primitive object via contact with a tool that transforms the object progressively to obtain the desired design. The analogy with the morphological operation of erosion is obvious. Nevertheless, few references about the relation between the morphological operations and the process of design and manufacturing can be found. The non-deterministic nature of classic mathematical morphology makes it very difficult to adapt their basic operations to the dynamics of concepts such as the ordered trajectory. A new geometric model is presented, inspired by the classic morphological paradigm, which can define objects and apply morphological operations that transform these objects. The model specializes in classic morphological operations, providing them with the determinism inherent in dynamic processes that require an order of application, as is the case for designing and manufacturing objects in professional computer-aided design and manufacturing (CAD/CAM) environments. The operators are boundary-based so that only the points in the frontier are handled. As a consequence, the process is more efficient and more suitable for use in CAD/CAM systems.

Forest-based supply chain modelling using the SimPy simulation framework

Proper management of supply chains is fundamental in the overall system performance of forestbased activities. Usually, efficient management techniques rely on a decision support software, which needs to be able to generate fast and effective outputs from the set of possibilities. In order to do this, it is necessary to provide accurate models representative of the dynamic interactions of systems. Due to forest-based supply chains’ nature, event-based models are more suited to describe their behaviours. This work proposes the modelling and simulation of a forestbased supply chain, in particular the biomass supply chain, through the SimPy framework. This Python based tool allows the modelling of discrete-event systems using operations such as events, processes and resources. The developed model was used to access the impact of changes in the daily working plan in three situations. First, as a control case, the deterministic behaviour was simulated. As a second approach, a machine delay was introduced and its implications in the plan accomplishment were analysed. Finally, to better address real operating conditions, stochastic behaviours of processing and driving times were simulated. The obtained results validate the SimPy simulation environment as a framework for modelling supply chains in general and for the biomass problem in particular.

Group-Based Symptom Trajectories in Indicated Prevention of Adolescent Depression

Background: Adolescent depression prevention research has focused on mean intervention outcomes, but has not considered heterogeneity in symptom course. Here, we empirically identify subgroups with distinct trajectories of depressive symptom change among adolescents enrolled in two indicated depression preven- tion trials and examine how cognitive-behavioral (CB) interventions and baseline predictors relate to trajectory membership. Methods: Six hundred thirty-one participants were assigned to one of three conditions: CB group intervention, CB bibliotherapy, and brochure control. We used group-based trajectory modeling to identify trajectories of depressive symptoms from pretest to 2-year follow-up. We examined associations between class membership and conditions using chi- square tests and baseline predictors using multinomial regressions. Results: We identified four trajectories in the full sample. Qualitatively similar trajectories were found in each condition separately. Two trajectories of positive symptom course (low-declining, high-declining) had declining symptoms and were dis- tinguished by baseline symptom severity. Two trajectories of negative course (high-persistent, resurging), respectively, showed no decline in symptoms or de- cline followed by symptom reappearance. Participants in the brochure control condition were significantly more likely to populate the high-persistent trajectory relative to either CB condition and were significantly less likely to populate the low-declining trajectory relative to CB group. Several baseline factors predicted trajectory classes, but gender was the most informative prognostic factor, with males having increased odds of membership in a high-persistent trajectory rel- ative to other trajectories. Conclusions: Findings suggest that CB preventive interventions do not alter the nature of trajectories, but reduce the risk that adolescents follow a trajectory of chronically elevated symptoms.