The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI

Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Gur, Tamer; Cowley, Andrew Peter; Li, Weizhong; Uludağ, Mahmut; Pundir, Sangya; Cham, Jennifer A.; McWilliam, Hamish; López, Rodrigo

doi:10.1093/nar/gkv316

Cited by 35 publications

(32 citation statements)

References 29 publications

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“…While our reference library represents a significant advance in plant DNA metabarcoding, our rbcL reference library and the ITS2 reference library of Sickel et al (2015) fall far short of being comprehensive. There are an estimated 450,000 flowering plant species on earth (Pimm (Benson et al, 2015), the DNA Data Bank of Japan (DDBJ; Mashima et al, 2015), and the European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Database (Squizzato et al, 2015), do not require researchers submitting sequences to provide links to voucher specimens or raw sequence data, and may include sequences with incorrect species identification or low-quality sequence data. Other databases, such as the Barcode of Life Database (BOLD; Ratnasingham and Hebert, 2007), have stringent quality control but fewer plant rbcL sequences than the NCBI database, and no plant ITS2 sequences.…”

Section: Discussionmentioning

confidence: 99%

How Many Plant Species are There, Where are They, and at What Rate are They Going Extinct?

Pimm

Joppa

2015

Annals of the Missouri Botanical Garden

178

104

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Section: Discussionmentioning

confidence: 99%

How Many Plant Species are There, Where are They, and at What Rate are They Going Extinct?

Pimm

Joppa

2015

Annals of the Missouri Botanical Garden

178

104

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“…Candidate proteins were classified as differentially expressed (exclusively in exosomes derived from dTGFBR2 or pTGFBR2 cells), if detected in at least three of four biological replicates. The raw data of MS proteomics are deposited to the ProteomeXchange Consortium via the PRIDE partner repository [30] with the project accession number: PXD005620 and project DOI: 10.6019/PXD005620 [31]. …”

Section: Methodsmentioning

confidence: 99%

TGFBR2-dependent alterations of exosomal cargo and functions in DNA mismatch repair-deficient HCT116 colorectal cancer cells

et al. 2017

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BackgroundColorectal cancers (CRCs) that lack DNA mismatch repair function exhibit the microsatellite unstable (MSI) phenotype and are characterized by the accumulation of frameshift mutations at short repetitive DNA sequences (microsatellites). These tumors recurrently show inactivating frameshift mutations in the tumor suppressor Transforming Growth Factor Beta Receptor Type 2 (TGFBR2) thereby abrogating downstream signaling. How altered TGFBR2 signaling affects exosome-mediated communication between MSI tumor cells and their environment has not been resolved. Here, we report on molecular alterations of exosomes shed by MSI cells and the biological response evoked in recipient cells.MethodsExosomes were isolated and characterized by electron microscopy, nanoparticle tracking, and western blot analysis. TGFBR2-dependent effects on the cargo and functions of exosomes were studied in a MSI CRC model cell line enabling reconstituted and inducible TGFBR2 expression and signaling. Microsatellite frameshift mutations in exosomal and cellular DNA were examined by PCR-based DNA fragment analysis and exosomal protein profiles were identified by mass spectrometry. Uptake of fluorescent-labeled exosomes by hepatoma recipient cells was monitored by confocal microscopy. TGFBR2-dependent exosomal effects on secreted cytokine levels of recipient cells were analyzed by Luminex technology and ELISA.ResultsFrameshift mutation patterns in microsatellite stretches of TGFBR2 and other MSI target genes were found to be reflected in the cargo of MSI CRC-derived exosomes. At the proteome level, reconstituted TGFBR2 expression and signaling uncovered two protein subsets exclusively occurring in exosomes derived from TGFBR2-deficient (14 proteins) or TGFBR2-proficient (five proteins) MSI donor cells. Uptake of these exosomes by recipient cells caused increased secretion (2–6 fold) of specific cytokines (Interleukin-4, Stem Cell Factor, Platelet-derived Growth Factor-B), depending on the TGFBR2 expression status of the tumor cell.ConclusionOur results indicate that the coding MSI phenotype of DNA mismatch repair-deficient CRC cells is maintained in their exosomal DNA. Moreover, we uncovered that a recurrent MSI tumor driver mutation like TGFBR2 can reprogram the protein content of MSI cell-derived exosomes and in turn modulate the cytokine secretion profile of recipient cells. Apart from its diagnostic potential, these TGFBR2-dependent exosomal molecular and proteomic signatures might help to understand the signaling routes used by MSI tumors.Graphical AbstractFricke et al. uncovered coding microsatellite instability-associated mutations of colorectal tumor driver genes like TGFBR2 in MSI tumor cellderived exosomes. Depending on the TGFBR2 expression status of their donor cells, shed exosomes show distinct proteomic signatures and promote altered cytokine secretion profiles in recipient cells. Electronic supplementary materialThe online version of this article (doi:10.1186/s12964-017-0169-y) contains supplementary material, which is avail...

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“…A current compromise is to rely on public sequence databases that may contain high coverage of species for a given habitat. For plants, the largest sources for reference sequencing data are the redundant repositories NCBI (Benson et al 2015), EMBL (Squizzato et al 2015), and DDBJ (Mashima et al 2015). There are over 32 million vascular plant nucleotide sequences deposited, although only a fraction of these represent DNA barcoding markers (see Table 1 for the number of sequences associated with each of the standard DNA barcoding markers).…”

Section: Component 2: Genetic Markersmentioning

confidence: 99%

Pollen DNA barcoding: current applications and future prospects

Bell

Vere

Keller

et al. 2016

Genome

201

170

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Identification of the species origin of pollen has many applications, including assessment of plant-pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.Key words: DNA metabarcoding, metagenomics, pollen, palynology, high-throughput sequencing, next-generation sequencing.Résumé : L'identification de l'espèce à l'origine d'un pollen se prête à de nombreuses applications dont la description des réseaux plante-pollinisateur, la reconstruction de communautés de plantes anciennes, l'authentification de produits, la surveillance des allergènes et les enquêtes médicolégales. Cependant, ces applications ont précédemment été limitées à l'identification du pollen par examen microscopique, un processus lent, à faible résolution taxonomique et qui compte peu de praticiens experts. Une alternative est l'identification du pollen par le recours aux codes à barres de l'ADN, une avenue qui permettrait de surmonter plusieurs de ces limitations. De récentes études ont montré qu'il était possible d'amplifier les marqueurs de codage tant chloroplastiques que nucléaires à partir du pollen. Ces récentes validations du métacodage à barres chez le pollen indiquent qu'il est maintenant opportun pour les chercheurs dans divers domaines de considérer l'emploi de ces méthodes dans leurs programmes de recherche. Dans cet article, les auteurs passent en revue le domaine naissant du codage à barres du pollen et discutent des nouvelles applications potentielles de cette technologie en mettant en lumière les limitations existantes ainsi que de futurs développements qui pourraient accroître son utilité dans un grand nombre d'applications. [Traduit par la Rédaction] Mots-clés : métacodage à barres, métagénomique, pollen, palynologie, séquençage à haut débit, séquençage de nouvelle génération.

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The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI

Cited by 35 publications

References 29 publications

How Many Plant Species are There, Where are They, and at What Rate are They Going Extinct?

How Many Plant Species are There, Where are They, and at What Rate are They Going Extinct?

TGFBR2-dependent alterations of exosomal cargo and functions in DNA mismatch repair-deficient HCT116 colorectal cancer cells

Pollen DNA barcoding: current applications and future prospects

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