Browsing by Subject "NGS"

Now showing 1 - 3 of 3
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    Blastocystis in free-ranging wild ruminant species across the Iberian Peninsula
    (BioMed Central, 2025-07-09) Figueiredo, Ana M.; Dashti, Alejandro; Maloney, Jenny G.; Molokin, Aleksey; George, Nadja S.; Köster, Pamela C.; Bailo, Begoña; Sánchez de las Matas, Ana; Habela, Miguel Ángel; Rivero Juarez, Antonio; Vicente, Joaquín; Serrano, Emmanuel; Arnal, María C.; Fernández de Luco, Daniel; Morrondo, Patrocinio; Armenteros, José A.; Balseiro, Ana; Cardona, Guillermo A.; Martínez-Carrasco Pleite, Carlos; Torres, Rita T.; Fonseca, Carlos; Mysterud, Atle; Carvalho, João; Calero-Bernal, Rafael; González Barrio, David; Santín, Mónica; Carmena, David; Sanidad Animal; Facultades de la UMU::Facultad de Veterinaria
    The growing wild ungulate populations across Europe represents an increasingly important source for the spread of zoonotic pathogens. Blastocystis is a common intestinal protist observed in humans and animals worldwide. Studies on Blastocystis occurrence and subtype (ST) diversity in free-ranging wild ruminants are lacking globally, and more data are needed to understand the epidemiological scenario in wild European ruminants. We collected 833 faecal samples from free-ranging wild angulates across Spain (n = 699) and Portugal (n = 134) between 1998 and 2021. Using conventional PCR and nextgeneration amplicon sequencing, Blastocystis was found in 13.8% (115/833; 95% CI: 11.5–16.3) of the wild ruminants analysed. Its occurrence was significantly higher in Portugal (38.1%, 51/134; 95% CI 29.8–46.8) than in Spain (9.2%, 64/699; 95% CI: 7.1–11.5). Fifteen Blastocystis STs, fourteen previously recognised (ST2, ST5, ST10, ST13, ST14, ST21, ST23–ST26, ST30, and ST42–ST44), and one novel (named ST49), were detected among the surveyed wild ruminant populations. Novel ST49 was described using Oxford Nanopore sequencing to produce full-length reference sequences of the small subunit ribosomal RNA gene. A greater ST diversity was observed in Spanish samples. Mixed infections were found in 58.3% (67/115) of the total Blastocystis-positive samples. Our results have enhanced the knowledge regarding Blastocystis occurrence and ST diversity and host preference present in wild ruminants from the Iberian Peninsula, which will assist in clarifying the relationships between the sylvatic and domestic cycles of this protist and may ultimately provide tools to help manage future public health epidemiological scenarios.
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    Open Access
    Monitoring of airborne biological particles in outdoor atmosphere. Part 2: metagenomics applied to urban environments
    (Institut d'Estudis Catalans, 2016-11-15) Núñez, Andrés; Amo de Paz, Guillermo; Rastrojo, Alberto; García, Ana M.; Alcamí, Antonio; Gutiérrez-Bustillo, A. Montserrat; Moreno, Diego A.; Genética y Microbiología
    The air we breathe contains microscopic biological particles such as viruses, bacteria, fungi and pollen, some of them with relevant clinic importance. These organisms and/or their propagules have been traditionally studied by different disciplines and diverse methodologies like culture and microscopy. These techniques require time, expertise and also have some important biases. As a consequence, our knowledge on the total diversity and the relationships between the different biological entities present in the air is far from being complete. Currently, metagenomics and next-generation sequencing (NGS) may resolve this shortage of information and have been recently applied to metropolitan areas. Although the procedures and methods are not totally standardized yet, the first studies from urban air samples confirm the previous results obtained by culture and microscopy regarding abundance and variation of these biological particles. However, DNA-sequence analyses call into question some preceding ideas and also provide new interesting insights into diversity and their spatial distribution inside the cities. Here, we review the procedures, results and perspectives of the recent works that apply NGS to study the main biological particles present in the air of urban environments.
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    Next generation sequencing identifies novel potential actionable mutations for grade I meningioma treatment
    (Universidad de Murcia, Departamento de Biologia Celular e Histiologia, 2020) Pepe, Francesco; Pisapia, Pasquale; Del Basso de Caro, Maria Laura; Conticelli, Floriana; Malapelle, Umberto; Troncone, Giancarlo; Martinez, Juan Carlos
    Meningiomas are common brain tumors that arise from the meningeal membranes that envelope the brain and spinal cord. The World Health Organization classifies these tumors into three histopathological grades. Because of tumor recurrence, treating meningiomas may be challenging even in well- differentiated grade I (GI) neoplasms. Indeed, around 5% of completely resected GI meningiomas relapse within 5 years. Therefore, identifying driver mutations in GI meningiomas through next generation sequencing (NGS) assays is paramount. The aim of this study was to validate the use of the 50-gene AmpliSeq Hotspot Cancer Panel v2 to identify the mutational status of 23 GI meningioma, namely, 12 non recurrent and 11 recurrent. In 18 out of the 23 GI meningiomas analyzed, we identified at least one gene mutation (78.2%). The most frequently mutated genes were c-kit (39.1%), ATM (26.1%), TP53 (26.1%), EGFR (26.1%), STK11 (21.7%), NRAS (17.4%), SMAD4 (13%), FGFR3 (13%), and PTPN11 (13%); less frequent mutations were SMARCB1 (8.7%), FLT3 (8.7%), KRAS (8.7%), FBWX7 (8.7%), ABL1 (8.7%), ERBB2 (8.7%), IDH1 (8.7%), BRAF (8.7%), MET (8.7%), HRAS (4.3%), RB1 (4.3%), CTNNB1 (4.3%), PIK3CA (4.3%), VHL (4.3%), KDR (4.3%), APC (4.3%), NOTCH1 (4.3%), JAK3 (4.3%), and SRC (4.3%). To our knowledge, mutations in all of these genes, except for TP53, STK11, SMARCB1, PIK3CA, VHL, and BRAF, have never been described before in meningiomas. Hence, these findings demonstrate the viability of NGS to detect new genetic alterations in GI meningiomas. Equally important, this technology enabled us to detect possible novel actionable mutations not previously associated with GI and for which selective inhibitors already exist