Zebrafish AID is capable of deaminating methylated deoxycytidines

Activation-induced cytidine deaminase (AID) deaminates deoxycytidine (dC) to deoxyuracil (dU) at immunoglobulin loci in B lymphocytes to mediate secondary antibody diversification. Recently, AID has been proposed to also mediate epigenetic reprogramming by demethylating methylated cytidines (mC) possibly through deamination. AID overexpression in zebrafish embryos was shown to promote genome demethylation through G:T lesions, implicating a deamination-dependent mechanism. We and others have previously shown that mC is a poor substrate for human AID. Here, we examined the ability of bony fish AID to deaminate mC. We report that zebrafish AID was unique among all orthologs in that it efficiently deaminates mC. Analysis of domain-swapped and mutant AID revealed that mC specificity is independent of the overall high-catalytic efficiency of zebrafish AID. Structural modeling with or without bound DNA suggests that efficient deamination of mC by zebrafish AID is likely not due to a larger catalytic pocket allowing for better fit of mC, but rather because of subtle differences in the flexibility of its structure.     

Screening for dihydrofolate reductase inhibitors using MOLPRINT 2D, a fast fragment-based method employing the naïve Bayesian classifier: limitations of the descriptor and the importance of balanced chemistry in training and test sets

A fragment-based similarity searching method, MOLPRINT 2D, was employed for virtual screening of Escherichia coli dihydrofolate reductase inhibitors. Using the original training set of 50,000 compounds, only marginal enrichment factors (between 1 and 3) could be achieved on the test library. The active structures contained in the training and test libraries represented different types of "chemistry", that is, different substructural features associated with activity. Training and test sets were pooled in a 2nd step and randomly split into training and test of equal size, with the objective of smoothing out the different chemical characteristics of both libraries. In a 10-fold cross-validation study on the new training and test sets, typically 10-fold enrichment could be found in the first 96 positions, 4-fold enrichment in the first 384 positions, and 3-fold enrichment in the first 1536 positions, corresponding to 6, 10, and 28 hits, respectively (out of a total of 307; activity defined as average residual activity of less than 80%). The conclusions are 2-fold. On one hand, the exact fragment-matching similarity searching method employed here is not capable of finding completely novel hit structures. On the other hand, this study emphasizes the requirement for a comparable distribution of chemical features of the training and test sets. MOLPRINT 2D is freely downloadable from http://www.cheminformatics.org.     

Kinematic networks

Motor control in primates relates to a system which is highly redundant from the mechanical point of view — redundancy coming from an imbalance between the set of independently controllable variables and the set of system variables. The consequence is the manifestation of a broad class of ill-posed problems, problems for which it is difficult to identify unique solutions. For example (i) the problem of determining the coordinated patterns of rotation of the arm joints for a planned trajectory of the hand; (ii) the problem of determining the distribution of muscle forces for a desired set of joint torques. Ill-posed problems, in general, require regularization methods which allow to spell acceptable, if not unique, solutions. In the case of the motor system, we propose that the basic regularization mechanism is provided by the potential fields generated by the elastic properties of muscles, according to an organizational principle that we call Passive Motion Paradigm. The physiological basis of this hypothesis is reviewed and a Kinematic Network (K-net) model is proposed that expresses the kinematic transformations and the causal relations implied by elasticity. Moreover, it is shown how K-nets can be obtained from a kinematic Body Model, in the context of a specific task. Two particularly significant results are: (i) the uniform treatment of closed as well as open kinematic chains, and (ii) the development of a new method for the automatic generation of kinematic equations with arbitrary topology. Moreover, the model is akin to the concept of motor equivalence in the sense that it provides families of motor equivalent trajectories parametrized by tunable motor impedances.     

Increased expression of HSP70 by colon cancer cells is not always associated with access to the dendritic cell cross-presentation pathway

Dendritic cells (DCs) are highly specialized antigen-presenting cells endowed with the unique ability to not only present exogenous antigens upon exposure to MHC II, but also to cross-present these upon exposure to MHC I. This property was exploited to generate the tumor-specific CD8 cytotoxic lymphocyte (CTL) response in DCs-based cancer vaccine protocols. In this context, the source of tumor antigens remains a critical challenge. A crude tumor in the context of danger signals is believed to represent an efficient source of tumor antigens (TAs) for DCs loading. In our previous work, increased DCs cross-presentation of antigens from necrotic gastric carcinoma cells paralleled up-regulation of the heat shock protein hsp70. We studied the expression of hsp70 on primary colon carcinoma cells and its relevance in the cross-priming of anti-tumor CTL by tumor-loaded DCs. Hsp70 was expressed on all three of the tumors studied, but was never detected in the peritumoral normal mucosa (NM). The uptake of the tumor induced a trend towards down-modulation of the monocyte-specific marker CD14, but had no effect on the chemokine receptors CCR4 and CCR7. The IFN-γ enzyme-linked immunospot assay (ELIspot) showed cross-priming of CTL by tumor-loaded but not NM-loaded DCs in four of the six cases studied. The CTL response generated in DC+tumor cultures was directed towards the tumor, but not towards NM, and it was characterized by refractoriness to polyclonal (Ca ionophores, PKC activators) stimuli. Of the three CTL-generating tumors, only one expressed hsp70. This data indicates a tumor-specific expression of hsp70, but does not support its relevance in the DC cross-presentation of TAs.     

Bone impairment in phenylketonuria is characterized by circulating osteoclast precursors and activated T cell increase

Background

Phenylketonuria (PKU) is a rare inborn error of metabolism often complicated by a progressive bone impairment of uncertain etiology, as documented by both ionizing and non- ionizing techniques.

Methodology

Peripheral blood mononuclear cell (PBMC) cultures were performed to study osteoclastogenesis, in the presence or absence of recombinant human monocyte-colony stimulating factor (M-CSF) and receptor activator of NFκB ligand (RANKL). Flow cytometry was utilized to analyze osteoclast precursors (OCPs) and T cell phenotype. Tumour necrosis factor α (TNF-α), RANKL and osteoprotegerin (OPG) were quantified in cell culture supernatants by ELISA. The effects of RANKFc and anti-TNF-α antibodies were also investigated to determine their ability to inhibit osteoclastogenesis. In addition, bone conditions and phenylalanine levels in PKU patients were clinically evaluated.

Principal Findings

Several in vitro studies in PKU patients'' cells identified a potential mechanism of bone formation inhibition commonly associated with this disorder. First, PKU patients disclosed an increased osteoclastogenesis compared to healthy controls, both in unstimulated and M-CSF/RANKL stimulated PBMC cultures. OCPs and the measured RANKL/OPG ratio were higher in PKU patients compared to healthy controls. The addition of specific antagonist RANKFc caused osteoclastogenesis inhibition, whereas anti-TNF-α failed to have this effect. Among PBMCs isolated from PKU patients, activated T cells, expressing CD69, CD25 and RANKL were identified. Confirmatory in vivo studies support this proposed model. These in vivo studies included the analysis of osteoclastogenesis in PKU patients, which demonstrated an inverse relation to bone condition assessed by phalangeal Quantitative Ultrasound (QUS). This was also directly related to non-compliance to therapeutic diet reflected by hyperphenylalaninemia.

Conclusions

Our results indicate that PKU spontaneous osteoclastogenesis depends on the circulating OCP increase and the activation of T cells. Osteoclastogenesis correlates with clinical parameters, suggesting its value as a diagnostic tool for an early assessment of an increased bone resorption in PKU patients.     

The HIV-1 Tat protein selectively enhances CXCR4 and inhibits CCR5 expression in megakaryocytic K562 cells

The hematopoietic compartments act as long-term reservoirs for human immunodeficiency virus type-1 (HIV-1). Although hematopoietic progenitor cells (HPCs) are rarely infectable, HPCs committed to the megakaryocytic lineage can be infected and support a productive infection by both the X4 and R5 strains of HIV-1. Indeed, in contrast to the CD34+ progenitors, the lineage-committed HPCs express high levels of the HIV-1 co-receptors, CXCR4 and CCR5. The HIV-1 transactivator (Tat) protein has been shown to alter co-receptor expression in T lymphocytes and macrophages. We hypothesized that Tat may regulate co-receptor expression in lineage-specific HPCs as well. We have monitored the effects of Tat protein on co-receptor expression and on lineage-specific differentiation, using the HPC cell line, K562. Butyric acid (BA)-induced erythroid differentiation in K562 cells was suppressed by 1-100 ng/ml of Tat, as evident from a 70-80% decrease in hemoglobin (Hb) production and a 10-30-fold decrease in glycophorin-A expression. However, Tat treatment enhanced phorbol myristate acetate (PMA)-induced megakaryocytic differentiation, as evident from a 180-210% increase in 3H-serotonin uptake and a 5-12-fold increase in CD61 expression. Tat did not significantly alter co-receptor expression in erythroid cells. However, Tat co-treatment profoundly effected both CXCR4 and CCR5 gene expression and protein levels in megakaryocytic cells. In PMA-stimulated cells, Tat increased CXCR4 and decreased in CCR5 expression, this was potentiated in cells chronically exposed to Tat. In conclusion, Tat protein suppresses erythroid and facilitates megakaryocytic differentiation of K562 cells. In megakaryocytic cells, Tat differentially effected CXCR4 and CCR5 expression. Because megakaryocytes may play a crucial role in HIV-1 infectivity in viral reservoirs, our findings implicate a role for Tat protein in dictating co-receptor usage in lineage-committed HPCs.