TGF-β3 and cancer: A review

With the development of growth factors and growth factor modulators as therapeutics for a range of disorders, it is prudent to consider whether modulating the growth factor profile in a tissue can influence tumour initiation or progression. As recombinant human TGF-β3 (avotermin) is being developed for the improvement of scarring in the skin it is important to understand the role, if any, of this cytokine in tumour progression.Elevated levels of TGF-β3 expression detected in late-stage tumours have linked this cytokine with tumourigenesis, although functional data to support a causative role are lacking. While it has proved tempting for researchers to interpret a ‘correlation’ as a ‘cause’ of disease, what has often been overlooked is the normal biological role of TGF-β3 in processes that are often subverted in tumourigenesis. Clarifying the role of this cytokine is complicated by inappropriate extrapolation of the data relating to TGF-β1 in tumourigenesis, despite marked differences in biology between the TGF-β isoforms. Indeed, published studies have indicated that TGF-β3 may actually play a protective role against tumourigenesis in a range of tissues including the skin, breast, oral and gastric mucosa. Based on currently available data it is reasonable to hypothesize that administration of acute low doses of exogenous TGF-β3 is unlikely to influence tumour initiation or progression.     

Semaphorin 3A: A new player in bone remodeling

Semaphorin 3A (Sema3A) is a protein identified originally as a diffusible axonal chemorepellent. Sema3A has multifunctional roles in embryonic development, immune regulation, vascularization, and oncogenesis. Bone remodeling consists of two phases: the removal of mineralized bone by osteoclasts and the formation of new bone by osteoblasts, and plays an essential role in skeletal diseases such as osteoporosis. Recent studies have shown that Sema3A is implicated in the regulation of osteoblastgenesis and osteoclastgenesis. Moreover, low bone mass in mice with specific knockout of Sema3A in the neurons indicates that Sema3A regulates bone remodeling indirectly. This review highlights recent advances on our understanding of the role of sema3A as a new player in the regulation of bone remodeling and proposes the potential of sema3A in the diagnosis and therapy of bone diseases.     

3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling

Electron microscopy (EM) is experiencing a revolution with the advent of a new generation of Direct Electron Detectors, enabling a broad range of large and flexible structures to be resolved well below 1 nm resolution. Although EM techniques are evolving to the point of directly obtaining structural data at near-atomic resolution, for many molecules the attainable resolution might not be enough to propose high-resolution structural models. However, accessing information on atomic coordinates is a necessary step toward a deeper understanding of the molecular mechanisms that allow proteins to perform specific tasks. For that reason, methods for the integration of EM three-dimensional maps with x-ray and NMR structural data are being developed, a modeling task that is normally referred to as fitting, resulting in the so called hybrid models. In this work, we present a novel application—3DIANA—specially targeted to those cases in which the EM map resolution is medium or low and additional experimental structural information is scarce or even lacking. In this way, 3DIANA statistically evaluates proposed/potential contacts between protein domains, presents a complete catalog of both structurally resolved and predicted interacting regions involving these domains and, finally, suggests structural templates to model the interaction between them. The evaluation of the proposed interactions is computed with DIMERO, a new method that scores physical binding sites based on the topology of protein interaction networks, which has recently shown the capability to increase by 200% the number of domain-domain interactions predicted in interactomes as compared to previous approaches. The new application displays the information at a sequence and structural level and is accessible through a web browser or as a Chimera plugin at http://3diana.cnb.csic.es.     

GLycol-EThanol-WAter (3:3:4); A SOlvent for SUdan BLack B STaining

The previously used supersaturated 60% isopropanol method (Lillie 1954, p. 303) protected the more readily soluble lipids from the solvent action of 70% alcohol but precipitation of dye particles within and around sections is sometimes a disturbing complication (cf. Vlachos 1959). The propylene glycol method of Chiffelle and Putt (Lillie, p. 304) has been found to remove much of the birefringent lipid from the sections. Glacial acetic acid dissolves most tissue lipids except those of the solvent-resistant ceroid or lipofuscin type. While solutions in 60-70% acetic acid conserve ordinary fats well (Sills and Marsh 1959) their effect on the more easily soluble lipids should be further explored.     

GLycol-EThanol-WAter (3:3:4); A SOlvent for SUdan BLack B STaining

The previously used supersaturated 60% isopropanol method (Lillie 1954, p. 303) protected the more readily soluble lipids from the solvent action of 70% alcohol but precipitation of dye particles within and around sections is sometimes a disturbing complication (cf. Vlachos 1959). The propylene glycol method of Chiffelle and Putt (Lillie, p. 304) has been found to remove much of the birefringent lipid from the sections. Glacial acetic acid dissolves most tissue lipids except those of the solvent-resistant ceroid or lipofuscin type. While solutions in 60–70% acetic acid conserve ordinary fats well (Sills and Marsh 1959) their effect on the more easily soluble lipids should be further explored.     

Signal-3L: A 3-layer approach for predicting signal peptides

Functioning as an "address tag" that directs nascent proteins to their proper cellular and extracellular locations, signal peptides have become a crucial tool in finding new drugs or reprogramming cells for gene therapy. To effectively and timely use such a tool, however, the first important thing is to develop an automated method for rapidly and accurately identifying the signal peptide for a given nascent protein. With the avalanche of new protein sequences generated in the post-genomic era, the challenge has become even more urgent and critical. In this paper, we have developed a novel method for predicting signal peptide sequences and their cleavage sites in human, plant, animal, eukaryotic, Gram-positive, and Gram-negative protein sequences, respectively. The new predictor is called Signal-3L that consists of three prediction engines working, respectively, for the following three progressively deepening layers: (1) identifying a query protein as secretory or non-secretory by an ensemble classifier formed by fusing many individual OET-KNN (optimized evidence-theoretic K nearest neighbor) classifiers operated in various dimensions of PseAA (pseudo amino acid) composition spaces; (2) selecting a set of candidates for the possible signal peptide cleavage sites of a query secretory protein by a subsite-coupled discrimination algorithm; (3) determining the final cleavage site by fusing the global sequence alignment outcome for each of the aforementioned candidates through a voting system. Signal-3L is featured by high success prediction rates with short computational time, and hence is particularly useful for the analysis of large-scale datasets. Signal-3L is freely available as a web-server at http://chou.med.harvard.edu/bioinf/Signal-3L/ or http://202.120.37.186/bioinf/Signal-3L, where, to further support the demand of the related areas, the signal peptides identified by Signal-3L for all the protein entries in Swiss-Prot databank that do not have signal peptide annotations or are annotated with uncertain terms but are classified by Signal-3L as secretory proteins are provided in a downloadable file. The large-scale file is prepared with Microsoft Excel and named "Tab-Signal-3L.xls", and will be updated once a year to include new protein entries and reflect the continuous development of Signal-3L.     

IRF-3 and Bax: A deadly affair

Comment on: Chattopadhyay S, Marques JT, Yamashita M, Peters KL, Smith K, Desai A, et al. Viral apoptosis is induced by IRF-3-mediated activation of Bax. EMBO J 2010; In press     

一种新型的组胺受体：H3受体

组胺受体有H_1、H_2两种亚型。最近又发现,组胺还有一种新型的受体,即H_3受体,它主要分布在中枢神经和外周神经末梢,参与组胺的合成和释放的负反馈调节过程。H_3受体的功能、性质类似于H_2受体,但它对组胺的敏感性要比H_1、H_2受体强。H_3受体的发现,为进一步研究组胺的生理、病理生理作用提供了新的基础。     

Hypoxia: A novel function for VIN3

VERNALIZATION INSENSITIVE 3 (VIN3) encodes a PHD domain chromatin remodelling protein that is induced in response to cold and is required for the establishment of the vernalization response in Arabidopsis thaliana.¹ Vernalization is the acquisition of the competence to flower after exposure to prolonged low temperatures, which in Arabidopsis is associated with the epigenetic repression of the floral repressor FLOWERING LOCUS C (FLC).^2,3 During vernalization VIN3 binds to the chromatin of the FLC locus,¹ and interacts with conserved components of Polycomb-group Repressive Complex 2 (PRC2).^4,5 This complex catalyses the tri-methylation of histone H3 lysine 27 (H3K27me3),^4,6,7 a repressive chromatin mark that increases at the FLC locus as a result of vernalization.^4,7–10 In our recent paper¹¹ we found that VIN3 is also induced by hypoxic conditions, and as is the case with low temperatures, induction occurs in a quantitative manner. Our experiments indicated that VIN3 is required for the survival of Arabidopsis seedlings exposed to low oxygen conditions. We suggested that the function of VIN3 during low oxygen conditions is likely to involve the mediation of chromatin modifications at certain loci that help the survival of Arabidopsis in response to prolonged hypoxia. Here we discuss the implications of our observations and hypotheses in terms of epigenetic mechanisms controlling gene regulation in response to hypoxia.Key words: arabidopsis, VIN3, FLC, hypoxia, vernalization, chromatin remodelling, survival     

Rabphilin-3A: A Multifunctional Regulator of Synaptic Vesicle Traffic

We have investigated the function of the synaptic vesicle protein Rabphilin-3A in neurotransmitter release at the squid giant synapse. Presynaptic microinjection of recombinant Rabphilin-3A reversibly inhibited the exocytotic release of neurotransmitter. Injection of fragments of Rabphilin-3A indicate that at least two distinct regions of the protein inhibit neurotransmitter release: the NH₂-terminal region that binds Rab3A and is phosphorylated by protein kinases and the two C2 domains that interact with calcium, phospholipid, and β-adducin. Each of the inhibitory fragments and the full-length protein had separate effects on presynaptic morphology, suggesting that individual domains were inhibiting a subset of the reactions in which the full-length protein participates. In addition to inhibiting exocytosis, constructs containing the NH₂ terminus of Rabphilin-3A also perturbed the endocytotic pathway, as indicated by changes in the membrane areas of endosomes, coated vesicles, and the plasma membrane. These results indicate that Rabphilin-3A regulates synaptic vesicle traffic and appears to do so at distinct stages of both the exocytotic and endocytotic pathways.     

3'-azido-3'-deoxythymidine binding to ribonuclease A: model for drug-protein interaction

Ribonuclease A (RNase A) with several high affinity binding sites is a possible target for many organic and inorganic molecules. 3'-Azido-3'-deoxythymidine (AZT) is the first clinically effective drug for the treatment of human immunodeficiency virus (HIV) infection. The drug interactions with protein and nucleic acids are associated with its mechanism of action in vivo. This study was designed to examine the interaction of AZT with RNase A under physiological conditions. Reaction mixtures of constant protein concentration (2%) and different drug contents (0.0001-0.1 mM) are studied by UV-visible, FTIR, and circular dichroism spectroscopic methods in order to determine the drug binding mode, the drug binding constant, and the effects of drug complexation on the protein and AZT conformations in aqueous solution. The spectroscopic results showed one major binding for the AZT-RNase complexes with an overall binding constant of 5.29 x 10(5) M(-1). An increase in the protein alpha helicity was observed upon AZT interaction, whereas drug sugar pucker remained in the C2'-endo/anti conformation in the AZT-RNase complexes.     

FOCAL3D: A 3-dimensional clustering package for single-molecule localization microscopy

Single-molecule localization microscopy (SMLM) is a powerful tool for studying intracellular structure and macromolecular organization at the nanoscale. The increasingly massive pointillistic data sets generated by SMLM require the development of new and highly efficient quantification tools. Here we present FOCAL3D, an accurate, flexible and exceedingly fast (scaling linearly with the number of localizations) density-based algorithm for quantifying spatial clustering in large 3D SMLM data sets. Unlike DBSCAN, which is perhaps the most commonly employed density-based clustering algorithm, an optimum set of parameters for FOCAL3D may be objectively determined. We initially validate the performance of FOCAL3D on simulated datasets at varying noise levels and for a range of cluster sizes. These simulated datasets are used to illustrate the parametric insensitivity of the algorithm, in contrast to DBSCAN, and clustering metrics such as the F1 and Silhouette score indicate that FOCAL3D is highly accurate, even in the presence of significant background noise and mixed populations of variable sized clusters, once optimized. We then apply FOCAL3D to 3D astigmatic dSTORM images of the nuclear pore complex (NPC) in human osteosaracoma cells, illustrating both the validity of the parameter optimization and the ability of the algorithm to accurately cluster complex, heterogeneous 3D clusters in a biological dataset. FOCAL3D is provided as an open source software package written in Python.     

NOO3D: A procedure to perform 3D species distribution models

There is consensus surrounding the need to include a third dimension when estimating Species Distribution Models (SDMs), which is of special interest for marine species. Application of the third dimension is, however, rarely available, thus users are obliged to manually combine 2D SDM outputs (i.e., suitability or presence/absence maps) for 3D distribution generation. Herein, the Niche of Occurrence 3D (NOO3D) is presented, which is a new, simple modelling procedure that provides 3D distributions using both 3D occurrence samples and environmental datasets that consist of one layer per depth value. NOO3D performance was evaluated using five virtual marine species to avoid errors associated with real data sets (three pelagic species, with wide, medium, and narrow distributions, respectively, a mesopelagic species and an abyssal species). These virtual species are distributed across the North Atlantic Ocean and were built to a 0.5° x 0.5° resolution and considering 49 depth levels (from 0.43 m to an undersea depth of 5274.7 m). NOO3D results were also compared to those provided by 3D Alpha Shapes and Maximum Entropy (MaxEnt). The True Positive Rate (TPR), or sensitivity, True Negative Rate (TNR), or specificity, False Positive Rate (FPR), or commission error, and False Negative Rate (FNR), or omission error, were employed in order to facilitate comparison between methods. MaxEnt performed best for TPR, TSS and FNR, and Alpha Shape 3D performed best for FPR and TNR. NOO3D was always the second-ranked method for all metrics considered, which indicates that it was the most suitable method. The provided results indicate that NOO3D can be considered a viable alternative in achieving three-dimensional species distribution models.