Dependence of Immunoglobulin Class Switch Recombination in B Cells on Vesicular Release of ATP and CD73 Ectonucleotidase Activity

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Deep sequencing of the X chromosome reveals the proliferation history of colorectal adenomas

Background

Mismatch repair deficient colorectal adenomas are composed of transformed cells that descend from a common founder and progressively accumulate genomic alterations. The proliferation history of these tumors is still largely unknown. Here we present a novel approach to rebuild the proliferation trees that recapitulate the history of individual colorectal adenomas by mapping the progressive acquisition of somatic point mutations during tumor growth.

Results

Using our approach, we called high and low frequency mutations acquired in the X chromosome of four mismatch repair deficient colorectal adenomas deriving from male individuals. We clustered these mutations according to their frequencies and rebuilt the proliferation trees directly from the mutation clusters using a recursive algorithm. The trees of all four lesions were formed of a dominant subclone that co-existed with other genetically heterogeneous subpopulations of cells. However, despite this similar hierarchical organization, the growth dynamics varied among and within tumors, likely depending on a combination of tumor-specific genetic and environmental factors.

Conclusions

Our study provides insights into the biological properties of individual mismatch repair deficient colorectal adenomas that may influence their growth and also the response to therapy. Extended to other solid tumors, our novel approach could inform on the mechanisms of cancer progression and on the best treatment choice.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0437-8) contains supplementary material, which is available to authorized users.     

Toward an accurate prediction of inter-residue distances in proteins using 2D recursive neural networks

Background

Protein inter-residue contact maps provide a translation and rotation invariant topological representation of a protein. They can be used as an intermediary step in protein structure predictions. However, the prediction of contact maps represents an unbalanced problem as far fewer examples of contacts than non-contacts exist in a protein structure. In this study we explore the possibility of completely eliminating the unbalanced nature of the contact map prediction problem by predicting real-value distances between residues. Predicting full inter-residue distance maps and applying them in protein structure predictions has been relatively unexplored in the past.

Results

We initially demonstrate that the use of native-like distance maps is able to reproduce 3D structures almost identical to the targets, giving an average RMSD of 0.5Å. In addition, the corrupted physical maps with an introduced random error of ±6Å are able to reconstruct the targets within an average RMSD of 2Å. After demonstrating the reconstruction potential of distance maps, we develop two classes of predictors using two-dimensional recursive neural networks: an ab initio predictor that relies only on the protein sequence and evolutionary information, and a template-based predictor in which additional structural homology information is provided. We find that the ab initio predictor is able to reproduce distances with an RMSD of 6Å, regardless of the evolutionary content provided. Furthermore, we show that the template-based predictor exploits both sequence and structure information even in cases of dubious homology and outperforms the best template hit with a clear margin of up to 3.7Å. Lastly, we demonstrate the ability of the two predictors to reconstruct the CASP9 targets shorter than 200 residues producing the results similar to the state of the machine learning art approach implemented in the Distill server.

Conclusions

The methodology presented here, if complemented by more complex reconstruction protocols, can represent a possible path to improve machine learning algorithms for 3D protein structure prediction. Moreover, it can be used as an intermediary step in protein structure predictions either on its own or complemented by NMR restraints.     

Deletion of the dual specific phosphatase-4 (DUSP-4) gene reveals an essential non-redundant role for MAP kinase phosphatase-2 (MKP-2) in proliferation and cell survival

Mitogen-activated protein kinase phosphatase-2 (MKP-2) is a type 1 nuclear dual specific phosphatase (DUSP) implicated in a number of cancers. We examined the role of MKP-2 in the regulation of MAP kinase phosphorylation, cell proliferation, and survival responses in mouse embryonic fibroblasts (MEFs) derived from a novel MKP-2 (DUSP-4) deletion mouse. We show that serum and PDGF induced ERK-dependent MKP-2 expression in wild type MEFs but not in MKP-2(-/-) MEFs. PDGF stimulation of sustained ERK phosphorylation was enhanced in MKP-2(-/-) MEFs, whereas anisomycin-induced JNK was only marginally increased. However, marked effects upon cell growth parameters were observed. Cellular proliferation rates were significantly reduced in MKP-2(-/-) MEFs and associated with a significant increase in cell doubling time. Infection with adenoviral MKP-2 reversed the decrease in proliferation. Cell cycle analysis revealed a block in G(2)/M phase transition associated with cyclin B accumulation and enhanced cdc2 phosphorylation. MEFs from MKP-2(-/-) mice also showed enhanced apoptosis when stimulated with anisomycin correlated with increased caspase-3 cleavage and γH2AX phosphorylation. Increased apoptosis was reversed by adenoviral MKP-2 infection and correlated with selective inhibition of JNK signaling. Collectively, these data demonstrate for the first time a critical non-redundant role for MKP-2 in regulating cell cycle progression and apoptosis.     

Reactivity of one-, two-, three- and four-electron reduced forms of α-[P2W18O62] generated by controlled potential electrolysis in water

One, two, three and four electron reduced forms of α-[P₂W₁₈O₆₂]⁶⁻ in aqueous acidic electrolyte media have been selectively generated by bulk electrolysis from a solution that has an initial pH of 3.6. The reactivities of the reduced polyoxometalate anions and identities of products formed in the presence and absence of dioxygen have been assessed via oxygen and hydrogen Clark-type electrodes, a pH electrode and rotating disk electrode voltammetry. [P₂W₁₈O₆₂]⁷⁻ is stable to protons but is slowly oxidized by dioxygen (timescale: hours to days) back to [P₂W₁₈O₆₂]⁶⁻. In contrast, [P₂W₁₈O₆₂]⁸⁻ reacts more rapidly with O₂ and slowly with H⁺, whereas generation of the [P₂W₁₈O₆₂]⁹⁻ and [P₂W₁₈O₆₂]¹⁰⁻ anion is accompanied by a large increase in pH and rapid reaction with O₂ or, in its absence, with H⁺. Consequently, it is concluded that photocatalytic reactions based upon [P₂W₁₈O₆₂]⁶⁻ chemistry are only likely to be of significance if [P₂W₁₈O₆₂]⁹⁻ or more highly reduced species are generated and form part of the catalytic cycle.     

The toxic effect of fluoride on MG-63 osteoblast cells is also dependent on the production of nitric oxide

Some soda-lime-phospho-silicate glasses, such as Hench's Bioglass(?) 45S5, form bone-like apatite on their surface when bound to living bone. To improve their osteointegration for clinical purposes, the fluoride insertion in their structure has been proposed, but we recently showed that fluoride causes oxidative damage in human MG-63 osteoblasts, via inhibition of pentose phosphate oxidative pathway (PPP) and its key enzyme glucose 6-phosphate dehydrogenase (G6PD). In the same cells we have now investigated the role of nitric oxide (NO) in these effects. Fluoride-containing bioactive glasses and NaF caused, as expected, release of lactate dehydrogenase in the extracellular medium, accumulation of intracellular malonyldialdehyde, inhibition of PPP and G6PD: we have now observed that these effects were significantly reverted not only by superoxide dismutase (SOD) plus catalase (scavengers of reactive oxygen species), but also by N-monomethyl l-arginine (l-NMMA, a NOS inhibitor) and 2-phenyl-4,4,5,5,-tetramethylimidazoline-1oxyl 3-oxide (PTIO, a NO scavenger). Moreover the two highest concentrations of both fluoride-containing bioglasses and NaF caused increase of nitrite (a stable derivative of NO) levels in the culture supernatant, which was inhibited by l-NMMA, erythrocytes, PTIO and SOD/catalase, and increase of intracellular NO synthase (NOS) activity. The incubation with bioglasses or NaF increased also the phosphorylation of Ser(1177) in the endothelial NOS isoform. Furthermore, the NO donor spermine NONOate was able to inhibit G6PD activity in vitro, and this effect was partly reverted by PTIO. Therefore our results suggest that most cytotoxic effects of fluoride are mediated by the production of NO: reactive oxygen species are important, causing NOS phosphorylation. We also observed, for the first time, that Tempol, but not SOD/catalase, besides inhibiting the oxidative stress induced by fluoride, also scavenges fluoride ions. For this reason it is not a selective inhibitor of the oxidative effects of fluoride.     

Giant Virus Megavirus chilensis Encodes the Biosynthetic Pathway for Uncommon Acetamido Sugars

Giant viruses mimicking microbes, by the sizes of their particles and the heavily glycosylated fibrils surrounding their capsids, infect Acanthamoeba sp., which are ubiquitous unicellular eukaryotes. The glycans on fibrils are produced by virally encoded enzymes, organized in gene clusters. Like Mimivirus, Megavirus glycans are mainly composed of virally synthesized N-acetylglucosamine (GlcNAc). They also contain N-acetylrhamnosamine (RhaNAc), a rare sugar; the enzymes involved in its synthesis are encoded by a gene cluster specific to Megavirus close relatives. We combined activity assays on two enzymes of the pathway with mass spectrometry and NMR studies to characterize their specificities. Mg534 is a 4,6-dehydratase 5-epimerase; its three-dimensional structure suggests that it belongs to a third subfamily of inverting dehydratases. Mg535, next in the pathway, is a bifunctional 3-epimerase 4-reductase. The sequential activity of the two enzymes leads to the formation of UDP-l-RhaNAc. This study is another example of giant viruses performing their glycan synthesis using enzymes different from their cellular counterparts, raising again the question of the origin of these pathways.     

ER Reorganization is Remarkably Induced in COS-7 Cells Accumulating Transmembrane Protein Receptors Not Competent for Export from the Endoplasmic Reticulum

The newly synthesized mutant L501fsX533 Frizzled-4 form and the alpha3beta4 nicotinic acetylcholine receptor expressed in the absence of nicotine accumulate in the endoplasmic reticulum of COS-7 cells and induce the formation of large areas of smooth and highly convoluted cisternae. This results in a generalized block of the transport to the Golgi complex of newly synthesized proteins. Intriguingly, both effects happen peculiarly in COS-7 cells; HeLa, Huh-7, and HEK293 cells expressing the two receptors at similar level than COS-7 cells show normal ER and normal transport toward the plasma membrane. These results question the conclusion that a dominant-negative mechanism would explain the dominance of the mutant L501fsX533 Fz4 allele in the transmission of a form of Familial exudative vitreoretinopathy. Moreover, they indicate that the coordination of endoplasmic reticulum homeostasis in COS-7 cells is particularly error prone. This finding suggests that COS-7 cells may be extremely useful to study the molecular mechanisms regulating endoplasmic reticulum size and architecture.