Área de Ciencias da Saúdehttp://hdl.handle.net/10347/28902024-03-29T10:52:47Z2024-03-29T10:52:47ZDetection of different Betanodavirus genotypes in wild fish from Spanish Atlantic coastal waters (Galicia, northwestern Spain)Vázquez Salgado, LucíaOlveira Hermida, José GabrielPereira Dopazo, CarlosBandín Matos, María Isabelhttp://hdl.handle.net/10347/332552024-03-21T09:21:45Z2023-01-01T00:00:00ZDetection of different Betanodavirus genotypes in wild fish from Spanish Atlantic coastal waters (Galicia, northwestern Spain)
Vázquez Salgado, Lucía; Olveira Hermida, José Gabriel; Pereira Dopazo, Carlos; Bandín Matos, María Isabel
Objective
The nervous necrosis virus (NNV; genus Betanodavirus) is an aquatic pathogen that is responsible for a neurological disease affecting marine fish. Despite its almost worldwide distribution, global warming could favor the spread of NNV to new areas, highlighting the importance of conducting epidemiological surveys on both wild and farmed marine fish species. In this study, we assessed NNV prevalence in wild fish caught along the Galician Atlantic coast.
Methods
In total, 1277 fish were analyzed by reverse transcription real-time polymerase chain reaction.
Result
Twenty two (1.72%) of those fish tested positive for NNV, including two species in which the pathogen had not yet been reported.
Conclusion
The reassortant RGNNV/SJNNV (red-spotted grouper NNV/striped jack NNV) was detected in 55% of NNV-positive individuals, while the remaining 45% harbored the SJNNV-type genome. Moreover, from European Pilchard Sardina pilchardus and Atlantic Mackerel Scomber scombrus, we isolated four reassortant strains that carried amino acid mutations at key sites related to NNV–host interaction.
2023-01-01T00:00:00ZCritical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysisRegueira Iglesias, AlbaBalsa Castro, CarlosBlanco Pintos, TrianaTomás Carmona, Inmaculadahttp://hdl.handle.net/10347/332452024-03-21T09:21:43Z2023-01-01T00:00:00ZCritical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis
Regueira Iglesias, Alba; Balsa Castro, Carlos; Blanco Pintos, Triana; Tomás Carmona, Inmaculada
The multi-batch reanalysis approach of jointly reevaluating gene/genome sequences from different works has gained particular relevance in the literature in recent years. The large amount of 16S ribosomal ribonucleic acid (rRNA) gene sequence data stored in public repositories and information in taxonomic databases of the same gene far exceeds that related to complete genomes. This review is intended to guide researchers new to studying microbiota, particularly the oral microbiota, using 16S rRNA gene sequencing and those who want to expand and update their knowledge to optimise their decision-making and improve their research results. First, we describe the advantages and disadvantages of using the 16S rRNA gene as a phylogenetic marker and the latest findings on the impact of primer pair selection on diversity and taxonomic assignment outcomes in oral microbiome studies. Strategies for primer selection based on these results are introduced. Second, we identified the key factors to consider in selecting the sequencing technology and platform. The process and particularities of the main steps for processing 16S rRNA gene-derived data are described in detail to enable researchers to choose the most appropriate bioinformatics pipeline and analysis methods based on the available evidence. We then produce an overview of the different types of advanced analyses, both the most widely used in the literature and the most recent approaches. Several indices, metrics and software for studying microbial communities are included, highlighting their advantages and disadvantages. Considering the principles of clinical metagenomics, we conclude that future research should focus on rigorous analytical approaches, such as developing predictive models to identify microbiome-based biomarkers to classify health and disease states. Finally, we address the batch effect concept and the microbiome-specific methods for accounting for or correcting them
2023-01-01T00:00:00ZAdapting an established Ampliseq microhaplotype panel to nanopore sequencing through direct PCRCasanova Adán, LucíaMosquera Miguel, AnaGonzález Bao, JavierAmbroa Conde, AdriánRuiz Ramírez, JorgeCabrejas Olalla, AmaiaGonzález Martín, E.Freire Aradas, Ana MaríaRodríguez López, AmeliaPhillips, Christopher PaulLareu Huidobro, María Victoriade la Puente Vila, María del Carmenhttp://hdl.handle.net/10347/332442024-03-21T09:21:43Z2023-01-01T00:00:00ZAdapting an established Ampliseq microhaplotype panel to nanopore sequencing through direct PCR
Casanova Adán, Lucía; Mosquera Miguel, Ana; González Bao, Javier; Ambroa Conde, Adrián; Ruiz Ramírez, Jorge; Cabrejas Olalla, Amaia; González Martín, E.; Freire Aradas, Ana María; Rodríguez López, Amelia; Phillips, Christopher Paul; Lareu Huidobro, María Victoria; de la Puente Vila, María del Carmen
We have adapted an established Ampliseq microhaplotype panel for nanopore sequencing with the Oxford Nanopore Technologies (ONT) system, as a cost-effective and highly scalable solution for forensic genetics applications. For this purpose, we designed a protocol combining direct PCR amplification from unextracted DNA with ONT library construction and sequencing using the MinION device and workflow. The analysis of reference samples at input amounts of 5–10 ng of DNA demonstrates stable coverage patterns, allele balance, and strand bias, reaching profile completeness and concordance rates of ∼95%. Similar levels were achieved when using direct-PCR from blood, buccal and semen swabs. Dilution series results indicate sensitivity is maintained down to 250 pg of input DNA, and informative profiles are produced down to 62.5 pg. Finally, we demonstrated the forensic utility of the nanopore workflow by analyzing two third degree pedigrees that showed low likelihood ratio values after the analysis of an extended panel of 38 STRs, achieving likelihood ratios 2–3 orders of magnitude higher when testing with the MinION–based haplotype data
2023-01-01T00:00:00ZReconstruction of plantar surgical defects with synthetic dermal matrix and split‐thickness skin grafts: A case series and functional podiatry outcomesGil-Pallares, PedroHeras-Sotos, Cristina de lashttp://hdl.handle.net/10347/332242024-03-21T09:21:42Z2023-01-01T00:00:00ZReconstruction of plantar surgical defects with synthetic dermal matrix and split‐thickness skin grafts: A case series and functional podiatry outcomes
Gil-Pallares, Pedro; Heras-Sotos, Cristina de las
Reconstruction of surgical defects after wide local excision of acral melanoma on the sole should allow patients to walk and bear weight. Moreover, certain options such as local transposition flaps can compromise follow-up. We present a case series of surgical defects on weight-bearing areas of the sole reconstructed using a synthetic dermal matrix and a split-thickness skin graft. This approach prevents surrounding tissue displacement and results in good functional outcomes assessed by baropodometry and computer-based podoscopy.
2023-01-01T00:00:00Z