1,721,078 research outputs found
Differential proteomics based on 2D-difference in-gel electrophoresis and tandem mass spectrometry for the elucidation of biological processes in antibiotic-producer bacterial strains
No full textProteomics based on 2D-Difference In Gel Electrophoresis (2D-DIGE) coupled with mass spectrometry (MS) procedures can be considered a â gold standardâ to determine quantitatively and comparatively protein abundances in cell extracts from different biological sources/conditions according to a gel-based approach. In particular, 2D-DIGE is used for protein specie separation, detection, and relative quantification, whenever tandem MS is used to obtain peptide sequence information that is managed according to bioinformatic procedures to identify the differentially represented protein species. The proteomic results consist of a dynamic portray of over- and down-represented protein species that, with the integration of gene ontology resources, allow obtaining a comprehensive understanding of the complex network of molecular signaling, regulatory circuits, and biochemical reactions occurring in cellular contexts. For this reason, proteomics has been widely used for studying molecular physiology of Gram-positive bacterial strains producing bioactive metabolites and belonging to actinomycete family. This highlighted the complex relationships linking overall regulatory processes and metabolic pathways to the biosynthesis of interesting bioactive molecules. In this chapter, we provide a detailed description of the procedures adopted to perform a differential proteomic analysis of the actinomycete Microbispora ATCC-PTA-5024, producing the promising NAI-107 lantibiotic. Although each experimental proteomic procedure has to be optimized to face the specific molecular characteristics of the organism under investigation, the protocols here described have also been used with minor modifications for proteomic studies on other bacterial strains, including the actinomycetes Streptomyces coelicolor, S. ambofaciens, Amycolatopsis balhimycina, and the Gram-negative proteobacteria Klebsiella oxytoca and Pseudoalteromonas haloplanktis
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Architecture of The Human Ape1 Interactome Defines Novel Cancers Signatures
Full text linkAPE1 is essential in cancer cells due to its central role in the Base Excision Repair pathway of DNA lesions and in the transcriptional regulation of genes involved in tumor progression/chemoresistance. Indeed, APE1 overexpression correlates with chemoresistance in more aggressive cancers, and APE1 protein-protein interactions (PPIs) specifically modulate different protein functions in cancer cells. Although important, a detailed investigation on the nature and function of protein interactors regulating APE1 role in tumor progression and chemoresistance is still lacking. The present work was aimed at analyzing the APE1-PPI network with the goal of defining bad prognosis signatures through systematic bioinformatics analysis. By using a well-characterized HeLa cell model stably expressing a flagged APE1 form, which was subjected to extensive proteomics analyses for immunocaptured complexes from different subcellular compartments, we here demonstrate that APE1 is a central hub connecting different subnetworks largely composed of proteins belonging to cancer-associated communities and/or involved in RNA- and DNA-metabolism. When we performed survival analysis in real cancer datasets, we observed that more than 80% of these APE1-PPI network elements is associated with bad prognosis. Our findings, which are hypothesis generating, strongly support the possibility to infer APE1-interactomic signatures associated with bad prognosis of different cancers; they will be of general interest for the future definition of novel predictive disease biomarkers. Future studies will be needed to assess the function of APE1 in the protein complexes we discovered. Data are available via ProteomeXchange with identifier PXD013368
AMOTL2 interaction with TAZ causes the inhibition of surfactant proteins expression in lung cells
No full textBackground: TAZ (Transcriptional co-Activator with PDZ-binding motif), is a biologically potent transcriptional coactivator and functions by binding to the PPXY motif present in several transcription factors. Notably, TAZ behaves as a transducer linking cytoplasmic signaling events to transcriptional regulation in the nucleus. Several different factors regulate TAZ expression and/or function. In particular, a major regulation of TAZ activity occurs through the Hippo pathway by a phosphorylation-mediated mechanism that causes its cytoplasmic sequestration or degradation. Results: Here we demonstrate that AMOTL2 robustly co-immunoprecipitates with TAZ, and their interaction is dependent on the WW domain of TAZ and the PPXY motif in the N-terminus of AMOTL2. Furthermore, we show that AMOTL2 colocalizes with TAZ in the cytoplasm of H441 human lung cells and regulates TAZ cytoplasm-to-nucleus translocation through direct protein-protein interaction. Interestingly, the overexpression of AMOTL2 inhibits the functional cooperation between the transcription factor TTF-1 and TAZ on the Surfactant C gene promoter, as well as the expression of other known target genes of these regulatory factors. Conclusions: Taken together, our results suggest an inhibitory role of AMOTL2 on TAZ ability to co-activate transcription and describe a different mechanism, Hippo pathway-independent, that modulates the activity of TAZ in lung cells through the interaction with Angiomotin-like 2 (AMOTL2)
Proteomic analysis reveals novel common genes modulated in both replicative and stress-induced senescence
No full textCellular senescence causes profound changes in gene expression profile. In this study, we used a combined 2D-DIGE and nanoLC-ESI-LIT-MS/MS approach to evaluate the proteomic changes occurring both in replicative and stress-induced senescence of human IMR90 cells. Twenty protein spots were identified as shifting their quantitative representation in the same direction (over- or down-represented) in both conditions of senescence, which were associated with 25 sequence entries. Dedicated experiments demonstrated that the decreased representation of a set of these proteins is associated with the down-regulation of the corresponding mRNAs, indicating that the regulation of these genes during the senescence process occurs at a transcriptional level. We also performed functional studies by silencing nine of these genes in young cells, which demonstrated that RNA interference-mediated knockdown of LEPRE1, LIMA1/EPLIN, MAGOHA and MAGOHB induces a premature senescent phenotype in IMR90 cells. Chromatin immunoprecipitation experiments indicated that the reduced expression of these four genes is associated with changes in the histone methylation pattern of their promoters, as proved by the occurrence of increased repressive H3K27me3 along with decreased active H3K4me3 marks, respectively
Sperm-attractant peptide influences the spermatozoa swimming behavior in internal fertilization in Octopus vulgaris
No full textVariations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Protective role of carbonic anhydrases III and VII in cellular defense mechanisms upon redox unbalance
Full text linkUnder oxidative stress conditions, several constitutive cellular defense systems are activated, which involve both enzymatic systems
and molecules with antioxidant properties such as glutathione and vitamins. In addition, proteins containing reactive sulfhydryl
groups may eventually undergo reversible redox modifications whose products act as protective shields able to avoid further
permanent molecular oxidative damage either in stressful conditions or under pathological circumstances. After the recovery of
normal redox conditions, the reduced state of protein sulfhydryl groups is restored. In this context, carbonic anhydrases (CAs)
III and VII, which are human metalloenzymes catalyzing the reversible hydration of carbon dioxide to bicarbonate and proton,
have been identified to play an antioxidant role in cells where oxidative damage occurs. Both proteins are mainly localized in
tissues characterized by a high rate of oxygen consumption, and contain on their molecular surface two reactive cysteine
residues eventually undergoing S-glutathionylation. Here, we will provide an overview on the molecular and functional features
of these proteins highlighting their implications into molecular processes occurring during oxidative stress conditions
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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