Aptamers are an innovative and promising tool for phytoplankton taxonomy and biodiversity research

Santamaria, Gianluca; Esposito, Carla Lucia; Cerchia, Laura; Benvenuto, Giovanna; Nanjappa, Deepak; Sarno, Diana; Zingone, Adriana; Franciscis, Vittorio de; d’Alcalà, Maurizio Ribera

doi:10.1080/02757540.2014.966700

Cited by 5 publications

(3 citation statements)

References 40 publications

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“…HTS was performed at rounds III, IV, V, VI, VII, VIII, IX, and X with MySeq Illumina sequencer, following the Illumina MySeq sequence preparation. Raw count reads were generated using python in-house script, then imported in R environment to produce the correlation plot [16] (The R Project for Statistical Computing. URL https://www.R-project.org/, (accessed on 21 May 2020).…”

Section: Cell-selexmentioning

confidence: 99%

Selection of a Nuclease-Resistant RNA Aptamer Targeting CD19

Esposito

Roosbroeck

Santamaria

et al. 2021

Cancers

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The transmembrane glycoprotein cluster of differentiation 19 (CD19) is a B cell–specific surface marker, expressed on the majority of neoplastic B cells, and has recently emerged as a very attractive biomarker and therapeutic target for B-cell malignancies. The development of safe and effective ligands for CD19 has become an important need for the development of targeted conventional and immunotherapies. In this regard, aptamers represent a very interesting class of molecules. Additionally referred to as ‘chemical antibodies’, they show many advantages as therapeutics, including low toxicity and immunogenicity. Here, we isolated a nuclease-resistant RNA aptamer binding to the human CD19 glycoprotein. In order to develop an aptamer also useful as a carrier for secondary reagents, we adopted a cell-based SELEX (Systematic Evolution of Ligands by EXponential Enrichment) protocol adapted to isolate aptamers able to internalise upon binding to their cell surface target. We describe a 2′-fluoro pyrimidine modified aptamer, named B85.T2, which specifically binds to CD19 and shows an exquisite stability in human serum. The aptamer showed an estimated dissociation constant (KD) of 49.9 ± 13 nM on purified human recombinant CD19 (rhCD19) glycoprotein, a good binding activity on human B-cell chronic lymphocytic leukaemia cells expressing CD19, and also an effective and rapid cell internalisation, thus representing a promising molecule for CD19 targeting, as well as for the development of new B-cell malignancy-targeted therapies.

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Section: Cell-selexmentioning

confidence: 99%

Selection of a Nuclease-Resistant RNA Aptamer Targeting CD19

Esposito

Roosbroeck

Santamaria

et al. 2021

Cancers

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“…The detection and quantification of species that are difficult to identify with morphology-based methods have been a goal for many years at LTER-MC, where a number of different attempts have been made to introduce adequate methods (McDonald et al 2007a, b, Barra et al 2013, Santamaria et al 2015, McNamee et al 2016. The direct access to molecules that are diagnostic for the individual taxa has opened a whole new range of possibilities for the study of microbial life, which has been scarcely known hitherto because of incomplete sampling, difficult cultivation and inadequate identification tools.…”

Section: Molecular Diversity: the Metabarcoding Approachmentioning

confidence: 99%

Time series and beyond: multifaceted plankton research at a marine Mediterranean LTER site

Zingone¹,

D’Alelio²,

Mazzocchi³

et al. 2019

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Plankton are a pivotal component of the diversity and functioning of coastal marine ecosystems. A long time-series of observations is the best tool to trace their patterns and variability over multiple scales, ultimately providing a sound foundation for assessing, modelling and predicting the effects of anthropogenic and natural environmental changes on pelagic communities. At the same time, a long time-series constitutes a formidable asset for different kinds of research on specific questions that emerge from the observations, whereby the results of these complementary studies provide precious interpretative tools that augment the informative value of the data collected. In this paper, we review more than 140 studies that have been developed around a Mediterranean plankton time series gathered in the Gulf of Naples at the station LTER-MC since 1984. These studies have addressed different topics concerning marine plankton, which have included: i) seasonal patterns and trends; ii) taxonomic diversity, with a focus on key or harmful algal species and the discovery of many new taxa; iii) molecular diversity of selected species, groups of species or the whole planktonic community; iv) life cycles of several phyto- and zooplankton species; and v) interactions among species through trophic relationships, parasites and viruses. Overall, the products of this research demonstrate the great value of time series besides the record of fluctuations and trends, and highlight their primary role in the development of the scientific knowledge of plankton much beyond the local scale.

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“…In almost all diatoms the zygote gives rise to vegetative cells instead, while resting stages are formed during asexual reproduction [ 20 , 21 ]. By contrast, sexual reproduction has not been found in the congeneric L. aporus, which despite a high morphological similarity, differs from L. danicus in several physiological and ecological characteristics [ 17 , 18 , 22 – 24 ]. To address functional differences between the two species, we cultivated them and sequenced their transcriptomes taking advantage of the Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP, [ 25 ]).…”

Section: Introductionmentioning

confidence: 99%

Diatom flagellar genes and their expression during sexual reproduction in Leptocylindrus danicus

et al. 2017

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BackgroundFlagella have been lost in the vegetative phase of the diatom life cycle, but they are still present in male gametes of centric species, thereby representing a hallmark of sexual reproduction. This process, besides maintaining and creating new genetic diversity, in diatoms is also fundamental to restore the maximum cell size following its reduction during vegetative division. Nevertheless, sexual reproduction has been demonstrated in a limited number of diatom species, while our understanding of its different phases and of their genetic control is scarce.ResultsIn the transcriptome of Leptocylindrus danicus, a centric diatom widespread in the world’s seas, we identified 22 transcripts related to the flagella development and confirmed synchronous overexpression of 6 flagellum-related genes during the male gamete formation process. These transcripts were mostly absent in the closely related species L. aporus, which does not have sexual reproduction. Among the 22 transcripts, L. danicus showed proteins that belong to the Intra Flagellar Transport (IFT) subcomplex B as well as IFT-A proteins, the latter previously thought to be absent in diatoms. The presence of flagellum-related proteins was also traced in the transcriptomes of several other centric species. Finally, phylogenetic reconstruction of the IFT172 and IFT88 proteins showed that their sequences are conserved across protist species and have evolved similarly to other phylogenetic marker genes.ConclusionOur analysis describes for the first time the diatom flagellar gene set, which appears to be more complete and functional than previously reported based on the genome sequence of the model centric diatom, Thalassiosira pseudonana. This first recognition of the whole set of diatom flagellar genes and of their activation pattern paves the way to a wider recognition of the relevance of sexual reproduction in individual species and in the natural environment.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4210-8) contains supplementary material, which is available to authorized users.

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Aptamers are an innovative and promising tool for phytoplankton taxonomy and biodiversity research

Cited by 5 publications

References 40 publications

Selection of a Nuclease-Resistant RNA Aptamer Targeting CD19

Selection of a Nuclease-Resistant RNA Aptamer Targeting CD19

Time series and beyond: multifaceted plankton research at a marine Mediterranean LTER site

Diatom flagellar genes and their expression during sexual reproduction in Leptocylindrus danicus

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