Inhibition of Mycobacterium tuberculosis tyrosine phosphatase PtpA by synthetic chalcones: Kinetics, molecular modeling, toxicity and effect on growth

Tuberculosis (TB) is a major cause of morbidity and mortality throughout the world, and it is estimated that one-third of the world`s population is infected with Mycobacterium tuberculosis. Among a series of tested compounds, we have recently identified five synthetic chalcones which inhibit the activity of M. tuberculosis protein tyrosine phosphatase A (PtpA), an enzyme associated with M. tuberculosis infectivity. Kinetic studies demonstrated that these compounds are reversible competitive inhibitors. In this work we also carried out the analysis of the molecular recognition of these inhibitors on their macromolecular target, PtpA, through molecular modeling. We observed that the predominant determinants responsible for the inhibitory activity of the chalcones are the positions of the two methoxyl groups at the A-ring, that establish hydrogen bonds with the amino acid residues Arg17, His49, and Thr12 in the active site of PtpA, and the substitution of the phenyl ring for a 2-naphthyl group as B-ring, that undergoes p stacking hydrophobic interaction with the Trp48 residue from PtpA. Interestingly, reduction of mycobacterial survival in human macrophages upon inhibitor treatment suggests their potential use as novel therapeutics. The biological activity, synthetic versatility, and low cost are clear advantages of this new class of potential tuberculostatic agents. (C) 2010 Elsevier Ltd. All rights reserved.

Human regulatory protein Ki-1/57 has characteristics of an intrinsically unstructured protein

The human protein Ki-1/57 was first identified through the cross reactivity of the anti-CD30 monoclonal antibody Ki-1; in Hodgkin lymphoma cells. The expression of Ki-1/57 in diverse cancer cells and its phosphorylation in peripheral blood leukocytes after mitogenic activation suggested its possible role in cell signaling. Ki-1/57 interacts with several other regulatory proteins involved in cellular signaling, transcriptional regulation and RNA metabolism, suggesting it may have pleiotropic functions. In a previous spectroscopic analysis, we observed a low content of secondary structure for Ki-1/57 constructs. Here, Circular dichroism experiments, in vitro RNA binding analysis, and limited proteolysis assays of recombinant Ki-1/57(122-413) and proteolysis assays of endogenous full length protein from human HEK293 cells suggested that Ki-1/57 has characteristics of an intrinsically unstructured protein. Small-angle X-ray scattering (SAXS) experiments were performed with the C-terminal fragment Ki-1/57(122-413). These results indicated an elongated shape and a partially unstructured conformation of the molecule in solution, confirming the characteristics of an intrinsically unstructured protein. Experimental curves together with ab initio modeling approaches revealed an extended and flexible molecule in solution. An elongated shape was also observed by analytical gel filtration. Furthermore, sedimentation velocity analysis suggested that Ki-1/57 is a highly asymmetric protein. These findings may explain the functional plasticity of Ki-1/57, as suggested by the wide array of proteins with which it is capable of interacting in yeast two-hybrid interaction assays.

Modeling dialogue with mixed initiative in design space exploration

Exploration with a generative formalism must necessarily account for the nature of interaction between humans and the design space explorer. Established accounts of design interaction are made complicated by two propositions in Woodbury and Burrow's Keynote on design space exploration. First, the emphasis on the primacy of the design space as an ordered collection of partial designs (version, alternatives, extensions). Few studies exist in the design interaction literature on working with multiple threads simultaneously. Second, the need to situate, aid, and amplify human design intentions using computational tools. Although specific research and practice tools on amplification (sketching, generation, variation) have had success, there is a lack of generic, flexible, interoperable, and extensible representation to support amplification. This paper addresses the above, working with design threads and computer-assisted design amplification through a theoretical model of dialogue based on Grice's model of rational conversation. Using the concept of mixed initiative, the paper presents a visual notation for representing dialogue between designer and design space formalism through abstract examples of exploration tasks and dialogue integration.

Human Sulfotransferases and Their Role in Chemical Metabolism

Sulfonation is an important reaction in the metabolism of numerous xenobiotics, drugs, and endogenous compounds. A supergene family of enzymes called sulfotransferases (SULTs) catalyze this reaction. In most cases, the addition of a sulfonate moiety to a compound increases its water solubility and decreases its biological activity. However, many of these enzymes are also capable of bioactivating procarcinogens to reactive electrophiles. In humans three SULT families, SULT1, SULT2, and SULT4, have been identified that contain at least thirteen distinct members. SULTs have a wide tissue distribution and act as a major detoxification enzyme system in adult and the developing human fetus. Nine crystal structures of human cytosolic SULTs have now been determined, and together with site-directed mutagenesis experiments and molecular modeling, we are now beginning to understand the factors that govern distinct but overlapping substrate specificities. These studies have also provided insight into the enzyme kinetics and inhibition characteristics of these enzymes. The regulation of human SULTs remains as one of the least explored areas of research in the field, though there have been some
recent advances on the molecular transcription mechanism controlling the individual SULT promoters. Interindividual variation in sulfonation capacity may be important in determining an individual’s response to xenobiotics, and recent studies have begun to suggest roles for SULT polymorphism in disease susceptibility. This review aims to provide a summary of our present understanding of the function of human cytosolic sulfotransferases.

Structural and functional properties of human multidrug resistance protein 1 (MRP1/ABCC1)

Multidrug ABC transporters such as P-glycoprotein (P-gp/MDR1/ABCB1) and multidrug resistance protein 1 (MRP1/ABCC1) play an important role in the extrusion of drugs from the cell and their overexpression can be a cause of failure of anticancer and antimicrobial chemotherapy. Recently, the mouse P-gp/Abcb1a structure has been determined and this has significantly enhanced our understanding of the structure-activity relationship (SAR) of mammalian ABC transporters. This paper highlights our current knowledge on the structural and functional properties and the SAR of human MRP1/ABCC1. Although the crystal structure of MRP1/ABCC1 has yet to be resolved, the current topological model of MRP1/ABCC1 contains two transmembrane domains (TMD1 and TMD2) each followed by a nucleotide binding domain (NBD) plus a third NH2-terminal TMD0. MRP1/ABCC1 is expressed in the liver, kidney, intestine, brain and other tissues. MRP1/ABCC1 transports a structurally diverse array of important endogenous substances (e.g. leukotrienes and estrogen conjugates) and xenobiotics and their metabolites, including various conjugates, anticancer drugs, heavy metals, organic anions and lipids. Cells that highly express MRP1/ABCC1 confer resistance to a variety of natural product anticancer drugs such as vinca alkaloids (e.g. vincristine), anthracyclines (e.g. etoposide) and epipodophyllotoxins (e.g. doxorubicin and mitoxantrone). MRP1/ABCC1 is associated with tumor resistance which is often caused by an increased efflux and decreased intracellular accumulation of natural product anticancer drugs and other anticancer agents. However, most compounds that efficiently reverse P-gp/ABCB1-mediated multidrug resistance have only low affinity for MRP1/ABCC1 and there are only a few effective and relatively specific MRP1/ABCC1 inhibitors available. A number of site-directed mutagenesis studies, biophysical and photolabeling studies, SAR and QSAR, molecular docking and homology modeling studies have documented the role of multiple residues in determining the substrate specificity and inhibitor selectivity of MRP1/ABCC1. Most of these residues are located in the TMs of TMD1 and TMD2, in particular TMs 4, 6, 7, 8, 10, 11, 14, 16, and 17, or in close proximity to the membrane/cytosol interface of MRP1/ABCC1. The exact transporting mechanism of MRP1/ABCC1 is unclear. MRP1/ABCC1 and other multidrug transporters are front-line mediators of drug resistance in cancers and represent important therapeutic targets in future chemotherapy. The crystal structure of human MRP1/ABCC1 is expected to be resolved in the near future and this will provide an insight into the SAR of MRP1/ABCC1 and allow for rational design of anticancer drugs and potent and selective MRP1/ABCC1 inhibitors.

Analysis of dynamic strains in tibia during human locomotion based on flexible multibody approach integrated with magnetic resonance imaging technique

Bone is known to adapt to the prevalent strain environment while the variation in strains, e.g., due to mechanical loading, modulates bone remodeling, and modeling. Dynamic strains rather than static strains provide the primary stimulus of bone functional adaptation. The finite element method can be generally used for estimating bone strains, but it may be limited to the static analysis of bone strains since the dynamic analysis requires expensive computation. Direct in vivo strain measurement, in turn, is an invasive procedure, limited to certain superficial bone sites, and requires surgical implementation of strain gauges and thus involves risks (e.g., infection). Therefore, to overcome difficulties associated with the finite element method and the in vivo strain measurements, the flexible multibody simulation approach has been recently introduced as a feasible method to estimate dynamic bone strains during physical activity. The purpose of the present study is to further strengthen the idea of using the flexible multibody approach for the analysis of dynamic bone strains. Besides discussing the background theory, magnetic resonance imaging is integrated into the flexible multibody approach framework so that the actual bone geometry could be better accounted for and the accuracy of prediction improved.

Preserving the environment and traditional communities : a land use change modeling approach

Human populations can cause serious damage to the natural environment. This, however, depends on the type of society and its size. Many traditional communities have a balanced relation with the environment, using practices for managing the soil, water and natural resources in order to satisfy their needs that are compatible to the general goals of environmental preservation.

The most usual approach to environmental conservation in the world sees human beings as intruders, potentially destroyers of the nature and, as a consequence, generally requires local population to be expelled from the protected regions. This situation has generated social conflicts because many protected areas, particularly in developing countries, are inhabited by indigenous or other traditional communities.

The disagreement about expelling or maintaining traditional communities in environmental conservation areas is strengthened by the lack of diagnostics on which changes are produced or suffered by communities in the region where they live. This paper presents a methodology developed to analyse land use dynamics in region with environmental conservation and traditional communities. We seek a better understanding of the way traditional communities use their space, the spatial pattern of land uses, which factors drive land use change, which impacts can be seen in those regions and identify the effects of conservation policies on land use dynamics.

The application of the method to the National Park of Superagui, Brazil, has successfully performed characterisation, analysis and simulation of land use dynamics in a region of environmental importance. Testing different scenarios has suggested that the adoption of a less restrictive policy for environmental conservation would have resulted in less social conflict with the same environmental efficiency than the established current policy.

Human action categorization using conditional random field

Automatic human action recognition has been a challenging issue in the field of machine vision. Some high-level features such as SIFT, although with promising performance for action recognition, are computationally complex to some extent. To deal with this problem, we construct the features based on the Distance Transform of body contours, which is relatively simple and computationally efficient, to represent human action in the video. After extracting the features from videos, we adopt the Conditional Random Field for modeling the temporal action sequences. The proposed method is tested with an available standard dataset. We also testify the robustness of our method on various realistic conditions, such as body occlusion or intersection.

Tracking-as-recognition for articulated full-body human motion analysis

This paper addresses the problem of markerless tracking of a human in full 3D with a high-dimensional (29D) body model Most work in this area has been focused on achieving accurate tracking in order to replace marker-based motion capture, but do so at the cost of relying on relatively clean observing conditions. This paper takes a different perspective, proposing a body-tracking model that is explicitly designed to handle real-world conditions such as occlusions by scene objects, failure recovery, long-term tracking, auto-initialisation, generalisation to different people and integration with action recognition. To achieve these goals, an action's motions are modelled with a variant of the hierarchical hidden Markov model The model is quantitatively evaluated with several tests, including comparison to the annealed particle filter, tracking different people and tracking with a reduced resolution and frame rate.

Segmentation of intentional human gestures for sports video annotation

We present results on the recognition of intentional human gestures for video annotation and retrieval. We define a gesture as a particular, repeatable, human movement having a predefined meaning. An obvious application of the work is in sports video annotation where umpire gestures indicate specific events. Our approach is to augment video with data obtained from accelerometers worn as wrist bands by one or more officials. We present the recognition performance using a Hidden Markov Model approach for gesture modeling with both isolated gestures and gestures segmented from a stream.

Does implicit motor imagery ability predict reaching correction efficiency? A test of recent models of human motor control

Neurocomputational models of reaching indicate that efficient purposive correction of movement midflight (e.g., online control) depends on one's ability to generate and monitor an accurate internal (neural) movement representation. In the first study to test this empirically, the authors investigated the relationship between healthy young adults’ implicit motor imagery performance and their capacity to correct their reaching trajectory. As expected, after controlling for general reaching speed, hierarchical regression demonstrated that imagery ability was a significant predictor of hand correction speed; that is, faster and more accurate imagery performance associated with faster corrections to reaching following target displacement at movement onset. They argue that these findings provide preliminary support for the view that a link exists between an individual's ability to represent movement mentally and correct movement online efficiently.

Modeling Potential Tiger Habitat in Hupingshan-Houhe and Mangshan-Nanling National Nature Reserves, China

After declining steadily for several decades, the South China tiger (Panthera tigris amoyensis) is now thought to be extinct in the wild. However, there is some hope of reintroduction, with Hupingshan-Houhe and Mangshan-Nanling National Nature Reserves in southern China seeming to hold the most promise. Our study used slope, elevation, vegetation, and landcover variables to construct a rough habitat suitability index for tigers in these two parks. According to our model, there are areas of suitable habitat within both parks. However, there are some important variables that we were unable to include in our model, such as human population density and prey availability. Considerable in-depth research will be necessary to evaluate the suitability of these locations before reintroduction is considered.

Transfer function-noise modeling and spatial interpolation to evaluate the risk of extreme (shallow) water-table levels in the Brazilian Cerrados

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Expression, purification, and circular dichroism analysis of human CDK9

The human cyclin-dependent kinase 9 (CDK9) protein was expressed in E coli BL21 using the pET23a vector at 30 degrees C. Several milligrams of protein were purified from soluble fraction using ionic exchange and ATP-affinity chromatography. The structural quality of recombinant CDK9 and the estimation of its secondary structure were obtained by circular dichroism. Structural models of CDK9 presented 26% of helices in agreement with the spectra by circular dichroism analysis. This is the first report on human CDK9 expression in Escherichia coli and structure analysis and provides the first step for the development of CDK9 inhibitors. (c) 2006 Elsevier B.V. All rights reserved.

Modeling and Experimental Aspects of Self-healing Bolted Joint through Shape Memory Alloy Actuators

Bolted joints are a form of mechanical coupling largely used in machinery due to their reliability and low cost. Failure of bolted joints can lead to catastrophic events, such as leaking, train derailments, aircraft crashes, etc. Most of these failures occur due to the reduction of the pre-load, induced by mechanical vibration or human errors in the assembly or maintenance process. This article investigates the application of shape memory alloy (SMA) washers as an actuator to increase the pre-load on loosened bolted joints. The application of SMA washer follows a structural health monitoring procedure to identify a damage (reduction in pre-load) occurrence. In this article, a thermo-mechanical model is presented to predict the final pre-load achieved using this kind of actuator, based on the heat input and SMA washer dimension. This model extends and improves on the previous model of Ghorashi and Inman [2004, "Shape Memory Alloy in Tension and Compression and its Application as Clamping Force Actuator in a Bolted Joint: Part 2 - Modeling," J. Intell. Mater. Syst. Struct., 15:589-600], by eliminating the pre-load term related to nut turning making the system more practical. This complete model is a powerful but complex tool to be used by designers. A novel modeling approach for self-healing bolted joints based on curve fitting of experimental data is presented. The article concludes with an experimental application that leads to a change in joint assembly to increase the system reliability, by removing the ceramic washer component. Further research topics are also suggested.