Cluster analysis and two-dimensional quantitative structure-activity relationship (2D-QSAR) of Pseudomonas aeruginosa deacetylase LpxC inhibitors

Compounds from a wide variety of structural classes inhibit Pseudomonas aeruginosa deacetylase LpxC. However, a single unified understanding of the relationship between the structures and activities of these compounds still eludes the researchers. We report herein, the development of cluster analysis-based 2D-QSAR models for LpxC inhibition. Principal component analysis (PCA), hierarchical cluster analysis (HCA), and genetic function approximation (GFA) were employed for the development of the QSAR model. The conventional 2D-QSAR model derived for the complete set of three-structural classes had unsatisfactory predictability with a correlation coefficient (r(2)) of 0.703 and a cross-validated correlation coefficient (q(2)) of 0.584. Descriptor-based cluster analysis indicated that the three-structural classes of LpxC inhibitors studied belonged to two clusters. Separate QSAR models for these two clusters showed substantially improved predictability with r(2) values of 0.904 and 0.944 and q(2) values of 0.805 and 0.906, respectively. Thus, we expect that compared to the conventional model, our two QSAR models can be better used to preliminarily screen molecules from a diverse chemical space while searching for novel LpxC inhibitors.

Quantitative structure activity relationship of benzoxazinone derivatives as neuropeptide Y Y5 receptor antagonists

Quantitative structure activity relationship (QSAR) has been established for 30 benzoxazinone derivatives acting as neuropeptide Y Y5 receptor antagonists. The genetic algorithm and multiple linear regression were used to generate the relationship between biological activity and calculated descriptors. Model with good statistical qualities was developed using four descriptors from topological, thermodynamic, spatial and electrotopological class. The validation of the model was done by cross validation, randomization and external test set prediction.

Progenitor cell-based myelination as a model for cell-based therapy of the central nervous system

Diseases of the brain and spinal cord are especially daunting challenges for cell-based strategies of repair, given the multiplicity of cell types within the adult central nervous system, and the precision with which they must interact in both space and time. Nonetheless, a number of diseases are especially appropriate for cell-based therapy, in particular those in which single phenotypes are lost. Foremost among these are the disorders of myelin, in which oligodendrocytes are the specific and often sole victims of the underlying disease process. These include not only the vascular, traumatic, and inflammatory demyelinations of adulthood, but also the congenital and childhood dysmyelinating syndromes of the pediatric leukodystrophies. These congenital disorders of myelin formation and maintenance may present especially compelling targets for cell-based neurological therapy.

Mrg19 depletion increasesS. cerevisiaelifespan by augmenting ROS defence

Caloric restriction (CR) is the most compelling example of lifespan extension by external manipulation. Although the molecular mechanisms remain unknown, the theory of hormesis has been invoked to explain the life promoting effects of CR. Hormesis is defined as the beneficial effects of low intensity stressor on a cell or organism. Mrg19 is a putative transcription factor that regulates carbon and nitrogen metabolism in yeast. In this study, we have found that deletion of MRG19 gene causes metabolic shift in yeast cells, leading to higher intracellular reactive oxygen species, augmentation of scavenging enzymes and longer lifespan compared to wild-type cells. All these results together suggest that similar to CR, depletion of Mrg19 leads to a condition of mild stress which in turn enhances vitality.

Sid4: A secreted vertebrate immunoglobulin protein with roles in zebrafish embryogenesis

The small members of the immunoglobulin superfamily (IGSF) are a molecularly diverse group of proteins composed solely of immunoglobulin domains. They may be secreted or tethered to the cell mebrane via GPI linkages and are proposed to have important functions in vivo. However, very few small IGSFs have been functionally characterized. During an ongoing in situ hybridization analysis of expressed sequence tags in zebrafish we identified secreted immunoglobulin domain 4 (sid4), a gene encoding a soluble vertebrate protein composed solely of four immunoglobulin domains. Throughout development, sid4 is expressed in regions of the embryo undergoing active cell division and migration. Functional analysis using morpholino antisense oligonucleotides demonstrates that timing of gene expression is normal in morphants, but these embryos are smaller and exhibit defects in epiboly and patterning of axial and prechordal mesoderm. Analyses of chordin, pax2, krox20, and dlx2 expression in morphants demonstrate that early brain patterning is normal but later organization of hindbrain neurons and development of cranial neural crest are perturbed. Levels of apoptosis in morphants were normal prior to 90% epiboly, but were elevated after 10 h post-fertilization (hpf). Apoptosis does not account for early patterning defects of axial mesoderm, but likely contributes to overall reduction in embryo size. Phylogenetic analysis demonstrates that Sid4 is strikingly similar to the fibronectin binding Ig domains of Perlecan/HSPG2. Overall, our data demonstrate a fundamental role for sid4, possibly as a co-factor in extracellular matrix (ECM) interactions, in processes underlying tissue patterning and organogenesis in a vertebrate.

Caloric restriction augments ROS defense in S. cerevisiae, by a Sir2p independent mechanism

Aging is associated with increased production of reactive oxygen species (ROS) and oxidation-induced damage to intracellular structures and membranes. Caloric restriction (CR) has been demonstrated to delay aging in a variety of species. Although the mechanisms of CR remain to be clearly elucidated, reductions in oxidative damage have been shown to increase lifespan in several model systems. Contrary to the general belief that ROS production is reduced in CR, this article provides evidence that not only oxygen consumption but ROS production is enhanced in the calorie restricted condition. To understand the biological mechanism underlying the anti aging action of CR, the role of scavenging enzymes was studied. It was found that super oxide dismutase (SOD1 and SOD2), catalase and glutathione peroxidase (GPx) all are over expressed in CR. We further investigated the role of Sir2, a potential effector of CR response in the activation of scavenging enzymes. No marked difference was found in CR mediated activation of SOD and catalase in the absence of Sir2. Our results suggest that in CR scavenging enzymes are activated by a Sir2 independent manner.

Finding Approximate POMDP solutions Through Belief Compression

Standard value function approaches to finding policies for Partially Observable Markov Decision Processes (POMDPs) are generally considered to be intractable for large models. The intractability of these algorithms is to a large extent a consequence of computing an exact, optimal policy over the entire belief space. However, in real-world POMDP problems, computing the optimal policy for the full belief space is often unnecessary for good control even for problems with complicated policy classes. The beliefs experienced by the controller often lie near a structured, low-dimensional subspace embedded in the high-dimensional belief space. Finding a good approximation to the optimal value function for only this subspace can be much easier than computing the full value function. We introduce a new method for solving large-scale POMDPs by reducing the dimensionality of the belief space. We use Exponential family Principal Components Analysis (Collins, Dasgupta & Schapire, 2002) to represent sparse, high-dimensional belief spaces using small sets of learned features of the belief state. We then plan only in terms of the low-dimensional belief features. By planning in this low-dimensional space, we can find policies for POMDP models that are orders of magnitude larger than models that can be handled by conventional techniques. We demonstrate the use of this algorithm on a synthetic problem and on mobile robot navigation tasks.

Shoulder and elbow function following Marchetti-Vicenzi humeral nail fixation

Humeral nailing has been associated with reduction of shoulder and elbow function. We present the results of fixation of 15 diaphyseal humeral fractures with Marchetti-Vicenzi nails (B Braun Medical Aesculap). Shoulder and elbow functions were assessed by the Constant shoulder and Mayo elbow scoring systems. The average Constant Shoulder score was good (82.5/100) and the average Mayo Elbow Score was excellent (95.4/100). The indications for surgery included nonunion, pathological fractures and poor fracture position. The mean follow-up was 67 weeks with an average interval to surgery of 19 weeks. The mean time to union was 19 weeks. All the fractures united without any patient requiring any further procedure. There were two postoperative radial nerve palsies and one median nerve palsy, however two patients had complete recovery and one had partial recovery of the radial nerve. There was one deep infection requiring removal of the implant. There were no implant failures. Based on our experience, the Marchetti-Vicenzi humeral nail appears as a relatively safe implant and its use has been associated with preservation of good shoulder and elbow functions.

Sir3p phosphorylation by the Slt2p pathway effects redistribution of silencing function and shortened lifespan

An organism's lifespan is modulated by environmental conditions. When nutrients are abundant, the metabolism of many organisms shifts to growth or reproduction at the expense of longer lifespan, whereas a scarcity of nutrients reverses this shift. These correlations suggest that organisms respond to environmental changes by altering their metabolism to promote either reproduction and growth or long life. The only previously reported signaling mechanism involved in this response is the nutrient-responsive insulin/insulin-like growth factor-1 receptor pathway. Here we report another pathway that controls the length of yeast lifespan. Commitment to cell growth activates the Slt2p MAP kinase pathway, which phosphorylates the transcriptional silencing protein Sir3p, resulting in a shorter lifespan. Elimination of the Sir3p phosphorylation site at Ser275 extended lifespan by 38%. Lifespan extension occurs by a mechanism that is independent of suppressing rDNA recombination. Thus, Slt2p is an enzymatic regulator of silencing function that couples commitment to cell growth and shorter lifespan.

Fibroma induction in rat skin following single or multiple doses of 1.0 GeV/nucleon 56Fe ions from the Brookhaven Alternating Gradient Synchrotron (AGS)

Rat skin was exposed to the plateau region of the 1.0 GeV/nucleon 56Fe beam at the Brookhaven AGS. Rats were irradiated or not with single of split doses of 56Fe or argon; some 56Fe-exposed rats were fed 250 ppm retinyl acetate continuously in the lab chow beginning 1 week before irradiation. All lesions were noted, photographed and identified for eventual histological diagnosis. The preponderance of the tumors so far are fibromas. The data show that single doses of 56Fe ions are 2 or 3 fold more effective than argon in producing tumors at 4.5 Gy but are about equally effective at 3.0 Gy and 9.0 Gy. The presence of 250 ppm retinyl acetate in the lab chow reduced the incidence of tumors by about 50-60% in comparison to groups exposed only to the radiation. These are preliminary findings based on only about one-fourth the eventual number of tumors expected.