Institution
Fundación Instituto Leloir
Facility•Buenos Aires, Argentina•
About: Fundación Instituto Leloir is a facility organization based out in Buenos Aires, Argentina. It is known for research contribution in the topics: Dentate gyrus & Neurogenesis. The organization has 702 authors who have published 1052 publications receiving 39299 citations.
Topics: Dentate gyrus, Neurogenesis, RNA, Arabidopsis, Gene
Papers published on a yearly basis
Papers
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TL;DR: This work contributes to the understanding of the different signals of evolution and also shows that it is possible to improve the detection of catalytic residues by integrating structural and higher order sequence evolutionary information with sequence conservation.
Abstract: Background: A large panel of methods exists that aim to identify residues with critical impact on protein function based on evolutionary signals, sequence and structure information. However, it is not clear to what extent these different methods overlap, and if any of the methods have higher predictive potential compared to others when it comes to, in particular, the identification of catalytic residues (CR) in proteins. Using a large set of enzymatic protein families and measures based on different evolutionary signals, we sought to break up the different components of the information content within a multiple sequence alignment to investigate their predictive potential and degree of overlap. Results: Our results demonstrate that the different methods included in the benchmark in general can be divided into three groups with a limited mutual overlap. One group containing real-value Evolutionary Trace (rvET) methods and conservation, another containing mutual information (MI) methods, and the last containing methods designed explicitly for the identification of specificity determining positions (SDPs): integer-value Evolutionary Trace (ivET), SDPfox, and XDET. In terms of prediction of CR, we find using a proximity score integrating structural information (as the sum of the scores of residues located within a given distance of the residue in question) that only the methods from the first two groups displayed a reliable performance. Next, we investigated to what degree proximity scores for conservation, rvET and cumulative MI (cMI) provide complementary information capable of improving the performance for CR identification. We found that integrating conservation with proximity scores for rvET and cMI achieved the highest performance. The proximity conservation score contained no complementary information when integrated with proximity rvET. Moreover, the signal from rvET provided only a limited gain in predictive performance when integrated with mutual information and conservation proximity scores. Combined, these observations demonstrate that the rvET and cMI scores add complementary information to the prediction system. Conclusions: This work contributes to the understanding of the different signals of evolution and also shows that it is possible to improve the detection of catalytic residues by integrating structural and higher order sequence evolutionary information with sequence conservation.
43 citations
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TL;DR: Recent advances are highlighted in the understanding of EXT modifications throughout the secretory pathway, EXT assembly in cell walls, and possible sensing mechanisms involving the Catharanthus roseus cell surface sensor receptor-like kinases located at the interface between the apoplast and the cytoplasmic side of the plasma membrane.
43 citations
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TL;DR: AMF plays a role in MSC recruitment towards HCC, however, its ability to increase MSC migration to HCC for therapeutic purposes merits further evaluation.
Abstract: Background and Aims
Several reports described the migration of human mesenchymal stromal cells (MSCs) towards tumor-released factors. Autocrine motility factor (AMF) is produced by several tumors including hepatocellular carcinoma (HCC). The aim of this study was to analyze AMF involvement on MSC migration towards human HCC.
43 citations
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TL;DR: Investigations on the function of Sudestada1 (Sud1), a Drosophila ribosomal oxygenase show that sud1 encodes a prolyl-hydroxylase that catalyzes posttranslational hydroxylation of a conserved residue in the small Ribosomal subunit protein RPS23.
Abstract: Genome sequences predict the presence of many 2-oxoglutarate (2OG)-dependent oxygenases of unknown biochemical and biological functions in Drosophila. Ribosomal protein hydroxylation is emerging as an important 2OG oxygenase catalyzed pathway, but its biological functions are unclear. We report investigations on the function of Sudestada1 (Sud1), a Drosophila ribosomal oxygenase. As with its human and yeast homologs, OGFOD1 and Tpa1p, respectively, we identified Sud1 to catalyze prolyl-hydroxylation of the small ribosomal subunit protein RPS23. Like OGFOD1, Sud1 catalyzes a single prolyl-hydroxylation of RPS23 in contrast to yeast Tpa1p, where Pro-64 dihydroxylation is observed. RNAi-mediated Sud1 knockdown hinders normal growth in different Drosophila tissues. Growth impairment originates from both reduction of cell size and diminution of the number of cells and correlates with impaired translation efficiency and activation of the unfolded protein response in the endoplasmic reticulum. This is accompanied by phosphorylation of eIF2α and concomitant formation of stress granules, as well as promotion of autophagy and apoptosis. These observations, together with those on enzyme homologs described in the companion articles, reveal conserved biochemical and biological roles for a widely distributed ribosomal oxygenase.
42 citations
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TL;DR: A decrease in N-glycan mannose content significantly diminishes in vivo glucosidase II–mediated deglucosylation rates but does not affect in vivo UDP-glucose:glycoprotein glucosyltransferase–mediated glucosolation, thus increasing the possibility of displaying monoglucosymated structures able to interact with calnexin/calreticulin for longer time periods.
Abstract: Glucosidase II (GII) sequentially removes the two innermost glucose residues from the glycan (Glc3Man9GlcNAc2) transferred to proteins. GII also participates in cycles involving the lectin/chaperones calnexin (CNX) and calreticulin (CRT) as it removes the single glucose unit added to folding intermediates and misfolded glycoproteins by the UDP-Glc:glycoprotein glucosyltransferase (UGGT). GII is a heterodimer in which the α subunit (GIIα) bears the active site, and the β subunit (GIIβ) modulates GIIα activity through its C-terminal mannose 6-phosphate receptor homologous (MRH) domain. Here we report that, as already described in cell-free assays, in live Schizosaccharomyces pombe cells a decrease in the number of mannoses in the glycan results in decreased GII activity. Contrary to previously reported cell-free experiments, however, no such effect was observed in vivo for UGGT. We propose that endoplasmic reticulum α-mannosidase–mediated N-glycan demannosylation of misfolded/slow-folding glycoproteins may favor their interaction with the lectin/chaperone CNX present in S. pombe by prolonging the half-lives of the monoglucosylated glycans (S. pombe lacks CRT). Moreover, we show that even N-glycans bearing five mannoses may interact in vivo with the GIIβ MRH domain and that the N-terminal GIIβ G2B domain is involved in the GIIα–GIIβ interaction. Finally, we report that protists that transfer glycans with low mannose content to proteins have nevertheless conserved the possibility of displaying relatively long-lived monoglucosylated glycans by expressing GIIβ MRH domains with a higher specificity for glycans with high mannose content.
42 citations
Authors
Showing all 707 results
Name | H-index | Papers | Citations |
---|---|---|---|
Jorge J. Casal | 61 | 182 | 10814 |
Silvia N.J. Moreno | 61 | 225 | 10585 |
Won Sang Park | 58 | 227 | 10501 |
Su Young Kim | 51 | 198 | 8829 |
Marcelo J. Yanovsky | 44 | 93 | 7949 |
Mario D. Galigniana | 40 | 99 | 5257 |
Eduardo M. Castaño | 40 | 89 | 7125 |
Andrea V. Gamarnik | 38 | 82 | 5896 |
Osvaldo L. Podhajcer | 35 | 122 | 4996 |
Alejandro F. Schinder | 34 | 64 | 10256 |
Juliana Idoyaga | 32 | 63 | 5326 |
Fernando Alberto Goldbaum | 32 | 103 | 3385 |
Fernando Juan Pitossi | 31 | 65 | 4489 |
Kevin Gaston | 29 | 78 | 2725 |
Jong Woo Lee | 29 | 77 | 3453 |