Neural development features: Spatio-temporal development of the Caenorhabditis elegans neuronal network

The nematode Caenorhabditis elegans, with information on neural connectivity, three-dimensional position and cell linage provides a unique system for understanding the development of neural networks. Although C. elegans has been widely studied in the past, we present the first statistical study from a developmental perspective, with findings that raise interesting suggestions on the establishment of long-distance connections and network hubs. Here, we analyze the neuro-development for temporal and spatial features, using birth times of neurons and their three-dimensional positions. Comparisons of growth in C. elegans with random spatial network growth highlight two findings relevant to neural network development. First, most neurons which are linked by long-distance connections are born around the same time and early on, suggesting the possibility of early contact or interaction between connected neurons during development. Second, early-born neurons are more highly connected (tendency to form hubs) than later born neurons. This indicates that the longer time frame available to them might underlie high connectivity. Both outcomes are not observed for random connection formation. The study finds that around one-third of electrically coupled long-range connections are late forming, raising the question of what mechanisms are involved in ensuring their accuracy, particularly in light of the extremely invariant connectivity observed in C. elegans. In conclusion, the sequence of neural network development highlights the possibility of early contact or interaction in securing long-distance and high-degree connectivity

3-Deazaneplanocin A (DZNep), an Inhibitor of the Histone Methyltransferase EZH2, Induces Apoptosis and Reduces Cell Migration in Chondrosarcoma Cells

ObjectiveGrowing evidences indicate that the histone methyltransferase EZH2 (enhancer of zeste homolog 2) may be an appropriate therapeutic target in some tumors. Indeed, a high expression of EZH2 is correlated with poor prognosis and metastasis in many cancers. In addition, 3-Deazaneplanocin A (DZNep), an S-adenosyl-L homocysteine hydrolase inhibitor which induces EZH2 protein depletion, leads to cell death in several cancers and tumors. The aim of this study was to determine whether an epigenetic therapy targeting EZH2 with DZNep may be also efficient to treat chondrosarcomas.MethodsEZH2 expression was determined by immunohistochemistry and western-blot. Chondrosarcoma cell line CH2879 was cultured in the presence of DZNep, and its growth and survival were evaluated by counting adherent cells periodically. Apoptosis was assayed by cell cycle analysis, Apo2.7 expression using flow cytometry, and by PARP cleavage using western-blot. Cell migration was assessed by wound healing assay.ResultsChondrosarcomas (at least with high grade) highly express EZH2, at contrary to enchondromas or chondrocytes. In vitro, DZNep inhibits EZH2 protein expression, and subsequently reduces the trimethylation of lysine 27 on histone H3 (H3K27me3). Interestingly, DZNep induces cell death of chondrosarcoma cell lines by apoptosis, while it slightly reduces growth of normal chondrocytes. In addition, DZNep reduces cell migration.ConclusionThese results indicate that an epigenetic therapy that pharmacologically targets EZH2 via DZNep may constitute a novel approach to treat chondrosarcomas

Polyisoprenylated benzophenone, garcinol, a natural histone acetyltransferase inhibitor, represses chromatin transcription and alters global gene expression

Histone acetylation is a diagnostic feature of transcriptionally active genes. The proper recruitment and function of histone acetyltransferases (HATs) and deacetylases (HDACs) are key regulatory steps for gene expression and cell cycle. Functional defects of either of these enzymes may lead to several diseases, including cancer. HATs and HDACs thus are potential therapeutic targets. Here we report that garcinol, a polyisoprenylated benzophenone derivative from Garcinia indica fruit rind, is a potent inhibitor of histone acetyltransferases p300 (IC50≈7 μM) and PCAF (IC50≈5 μM) both in vitro and in vivo. The kinetic analysis shows that it is a mixed type of inhibitor with an increased affinity for PCAF compared with p300. HAT activity-dependent chromatin transcription was strongly inhibited by garcinol, whereas transcription from DNA template was not affected. Furthermore, it was found to be a potent inducer of apoptosis, and it alters (predominantly down-regulates) the global gene expression in HeLa cells

Clostridium difficile infection.

Infection of the colon with the Gram-positive bacterium Clostridium difficile is potentially life threatening, especially in elderly people and in patients who have dysbiosis of the gut microbiota following antimicrobial drug exposure. C. difficile is the leading cause of health-care-associated infective diarrhoea. The life cycle of C. difficile is influenced by antimicrobial agents, the host immune system, and the host microbiota and its associated metabolites. The primary mediators of inflammation in C. difficile infection (CDI) are large clostridial toxins, toxin A (TcdA) and toxin B (TcdB), and, in some bacterial strains, the binary toxin CDT. The toxins trigger a complex cascade of host cellular responses to cause diarrhoea, inflammation and tissue necrosis - the major symptoms of CDI. The factors responsible for the epidemic of some C. difficile strains are poorly understood. Recurrent infections are common and can be debilitating. Toxin detection for diagnosis is important for accurate epidemiological study, and for optimal management and prevention strategies. Infections are commonly treated with specific antimicrobial agents, but faecal microbiota transplants have shown promise for recurrent infections. Future biotherapies for C. difficile infections are likely to involve defined combinations of key gut microbiota

Soluble sugars and germination of Annona emarginata (Schltdl.) H. Rainer seeds submitted to immersion in GA3 up to different water contents

The objective of this study was to evaluate the effect of different water contents achieved by Annona emarginata (Schltdl.) H. Rainer seeds during immersion in GA3 solutions, in variation of soluble sugars levels and germination. Seeds with 10% of initial water content were submitted to imbibition in GA3 solutions with concentrations of 0; 250; 500; 750 and 1000 mg L-1 and when they reached the water content of 15%, 20%, 25%, 30% and 35%, the quantification of soluble sugars levels and germination test were performed. Seeds immersed up to they reach 15% of water with GA3 and immersed up to the water acquisition of 20% without GA3, presented higher soluble sugars levels and germination percentage, which were decreased when the seeds reached 30% and 35% of water, independently of the presence of the plant growth regulator. It was conclude that different water contents reached by the seeds in immersion treatments with GA3 affect the soluble sugars levels and germination percentage of Annona emarginata seeds. Thus, in treatments with Annona emarginata, the seeds must remain immersed in water without GA3 up to they reach 20% of water, as higher water contents (35%) reduce the soluble sugars levels and the seed germination percentage.O objetivo deste trabalho foi avaliar o efeito de diferentes teores de água atingidos pelas sementes de Annona emarginata (Schltdl.) H. Rainer durante a imersão em soluções de GA3, na variação dos teores de açúcares solúveis e na germinação. Sementes com teor de água inicial de 10% foram colocadas para embeber em soluções com as concentrações de 0; 250; 500; 750 e 1.000 mg L-1 de GA3, e ao atingirem os teores de 15%, 20%, 25%, 30% e 35% de água, procedeu-se à quantificação dos teores de açúcares solúveis e ao teste de germinação. As sementes imersas até atingirem 15% de água com a adição de GA3 e imersas até a aquisição de 20% de água sem a adição de GA3 apresentaram maiores teores de açúcares solúveis e porcentagens de germinação, os quais foram reduzidos à medida que as sementes atingiram 30% e 35% de água, independentemente do uso do regulador vegetal. Conclui-se que os diferentes teores de água alcançados pelas sementes nos tratamentos de imersão afetam os teores de açúcares solúveis e a germinação de sementes de Annona emarginata. Assim, em tratamentos com Annona emarginata, as sementes devem permancer imersas na água sem a adição de GA3 até a aquisição de 20% de água, uma vez que elevados teores de água (35%) reduzem os teores de açúcares solúveis totais e a porcentagem de germinação das sementes.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)UNESP Biosciences Institute Graduation Program on Biological SciencesUNESP Biosciences Institute Botany DepartmentUNESP Biosciences Institute Graduation Program on Biological SciencesUNESP Biosciences Institute Botany DepartmentCNPq: 553428/2010-

PMeS: Prediction of Methylation Sites Based on Enhanced Feature Encoding Scheme

Protein methylation is predominantly found on lysine and arginine residues, and carries many important biological functions, including gene regulation and signal transduction. Given their important involvement in gene expression, protein methylation and their regulatory enzymes are implicated in a variety of human disease states such as cancer, coronary heart disease and neurodegenerative disorders. Thus, identification of methylation sites can be very helpful for the drug designs of various related diseases. In this study, we developed a method called PMeS to improve the prediction of protein methylation sites based on an enhanced feature encoding scheme and support vector machine. The enhanced feature encoding scheme was composed of the sparse property coding, normalized van der Waals volume, position weight amino acid composition and accessible surface area. The PMeS achieved a promising performance with a sensitivity of 92.45%, a specificity of 93.18%, an accuracy of 92.82% and a Matthew’s correlation coefficient of 85.69% for arginine as well as a sensitivity of 84.38%, a specificity of 93.94%, an accuracy of 89.16% and a Matthew’s correlation coefficient of 78.68% for lysine in 10-fold cross validation. Compared with other existing methods, the PMeS provides better predictive performance and greater robustness. It can be anticipated that the PMeS might be useful to guide future experiments needed to identify potential methylation sites in proteins of interest. The online service is available at http://bioinfo.ncu.edu.cn/inquiries_PMeS.aspx

Application of recombinant TAF3 PHD domain instead of anti-H3K4me3 antibody

BACKGROUND: Histone posttranslational modifications (PTMs) represent a focal point of chromatin regulation. The genome-wide and locus-specific distribution and the presence of distinct histone PTMs is most commonly examined with the application of histone PTM-specific antibodies. In spite of their central role in chromatin research, polyclonal antibodies suffer from disadvantages like batch-to-batch variability and insufficient documentation of their quality and specificity. RESULTS: To mitigate some of the pitfalls of using polyclonal antibodies against H3K4me3, we successfully validated the application of a recombinant TAF3 PHD domain as anti-H3K4me3 affinity reagent in peptide array, western blot and ChIP-like experiments coupled with qPCR and deep sequencing. CONCLUSIONS: The successful addition of the TAF3 PHD domain to the growing catalog of recombinant affinity reagents for histone PTMs could help to improve the reproducibility, interpretation and cross-laboratory validation of chromatin data. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13072-016-0061-9) contains supplementary material, which is available to authorized users