Search results for "next-generation"
showing 10 items of 80 documents
Taxidermal Preparations of an Extinct Sicilian Wolf Population (Canis lupus Linnaeus, 1758): Biological Studies and Restoration
2022
In last decades, biotechnologies have enabled a deep development of knowledge in all fields of life sciences, allowing the collection of a wide range of data. Furthermore, the relationship between scientific investigations and conservation actions of cultural heritage is increasingly consolidated and now it is one of the peculiar points both for sustainable restoration and use of the cultural asset, also evaluating the cultural assets as source of biological information. In this study, Sicilian wolf (Canis lupus) specimens conserved in Sicilian Natural Museums, become a source of biological information on Sicilian biodiversity, establishing specific conservative protocol developed cooperati…
The molecular profiling of solid tumors by liquid biopsy: a position paper of the AIOM–SIAPEC-IAP–SIBioC–SIC–SIF Italian Scientific Societies
2021
The term liquid biopsy (LB) refers to the use of various biological fluids as a surrogate for neoplastic tissue to achieve information for diagnostic, prognostic and predictive purposes. In the current clinical practice, LB is used for the identification of driver mutations in circulating tumor DNA derived from both tumor tissue and circulating neoplastic cells. As suggested by a growing body of evidence, however, there are several clinical settings where biological samples other than tissue could be used in the routine practice to identify potentially predictive biomarkers of either response or resistance to targeted treatments. New applications are emerging as useful clinical tools, and o…
Targeted NGS for species level phylogenomics: “made to measure” or “one size fits all”?
2017
Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools, or custom made for particular clades at considerably greater effort. We applied custom made scripts to select sets of homologous sequence markers from transcriptome and WGS data for use in the flowering plant genus Erica (Ericaceae). We compared the resulting targets to those that would be selected both using different available tools (Hyb-Seq; M…
Lightweight LCP construction for next-generation sequencing datasets
2012
The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing the longest common prefix array (LCP) of such a collection would facilitate the rapid computation of maximal exact matches, shortest unique substrings and shortest absent words. CPU-efficient algorithms for computing the LCP of a string have been described in the literature, but require the presence in RAM of large data structures. This prevents such methods from being feasible for NGS datasets. In this paper we propose the first lightweight method that simultaneously computes, via sequential scans, the LCP and B…
Temporal dynamics of soil bacterial communities at a landscape scale: dependence to soil properties and agricultural practices.
2019
International audience; Soil microbial communities play a major role in agricultural functions and are an efficient indicator to evaluate the impacts of agricultural practices on soils. Studies on wide scales ranging from landscape to countries demonstrated that soil microbial communities were heterogeneously distributed in space under the dependence of soil properties (e.g. pH, soil texture, Organic matter Content) and agricultural practices. However, temporal dynamics of soil microbial communities at a landscape scale still need to be documented in order to go further in evaluating the sustainability of agricultural practices. In this extensive monitoring study, we focused on landscape dy…
Tecnologías de secuenciación masiva y PCR digital en la detección de ADN tumoral procedente de tejido y plasma en pacientes de colon localizado
2022
El cáncer de colon se sitúa como uno de los tumores más relevantes a nivel social, con una tasa de entre el 30 y 50% de recaídas tras la resección. Como herramienta de estudio en este tumor, la biopsia líquida se ha abierto paso en diferentes ámbitos, tales como la detección de la heterogeneidad tumoral o la enfermedad mínima residual (EMR). El fundamento de esta estrategia es detectar el ADN tumoral circulante (ctDNA), que se encuentra diluido en el ADN libre circulante (cfDNA), siendo necesario el uso de tecnologías aptas para la detección a frecuencias bajo el 1%. La hipótesis de esta tesis se apoya en variantes somáticas para detectar el ctDNA y definir la heterogeneidad tumoral, la EMR…
A multi-omic liquid biopsy-based signature as a valuable tool to assess minimal residual disease in localised colorectal cancer
2019
El cáncer colorrectal (CCR) es un importante problema de salud pública. Más de 1.2 millones de pacientes se diagnostican de CCR cada año, y más de 600.000 mueren a causa de la enfermedad. El pronóstico de los pacientes con CCR ha mejorado durante las últimas décadas, con una supervivencia a los 5 años que ha alcanzado casi el 65% en países desarrollados. El estadio al diagnóstico es actualmente el factor pronóstico más importante. Aunque la clasificación clásica de estadiaje proporciona información pronóstica y guía las decisiones terapéuticas, no disponemos hoy en día de marcadores predictivos de la respuesta y del resultado clínico de la terapia individual del paciente. Esto es relevante …
Neoantigens Generated by Individual Mutations and Their Role in Cancer Immunity and Immunotherapy
2017
Recent preclinical and clinical studies have proved the long-standing hypothesis that tumors elicit adaptive immune responses and that the antigens driving effective T-cell response are neoantigens, i.e., peptides that are generated from somatically mutated genes. Hence, the characterization of neoantigens and the identification of the immunogenic ones are of utmost importance for improving cancer immunotherapy and broadening its efficacy to a larger fraction of patients. In this review, we first introduce the methods used for the quantification of neoantigens using next-generation sequencing data and then summarize results obtained using these tools to characterize the neoantigen landscape…
Deep sequencing of the human retinae reveals the expression of odorant receptors
2017
Several studies have demonstrated that the expression of odorant receptors (ORs) occurs in various tissues. These findings have served as a basis for functional studies that demonstrate the potential of ORs as drug targets for a clinical application. To the best of our knowledge, this report describes the first evaluation of the mRNA expression of ORs and the localization of OR proteins in the human retina that set a stage for subsequent functional analyses. RNA-Sequencing datasets of three individual neural retinae were generated using Next-generation sequencing and were compared to previously published but reanalyzed datasets of the peripheral and the macular human retina and to reference…
Grazing intensity in subarctic tundra affects the temperature adaptation of soil microbial communities
2015
Abstract Grazing by large ungulates, such as reindeer (Rangifer tarandus L.), in subarctic tundra exerts a considerable effect on the soil microclimate. Because of higher insulation by the aboveground vegetation in light versus heavily grazed areas, soil temperatures during the growing season are considerably higher under heavy grazing. Here, we hypothesized that these grazer-induced changes in soil microclimate affect the temperature sensitivity of soil microbial activity. To test this hypothesis, we conducted soil incubations at different temperatures (4 °C, 9 °C and 14 °C) for six weeks using soils from sites with contrasting long-term grazing intensities. Microbial respiration at low te…