The goal of this chapter is to provide a framework of sequential steps for small RNA (sRNA) analysis in filamentous fungi. Here, we present protocols for (1) comparative analysis of sRNAs in different conditions, (2) comparisons of sRNA libraries to RNAseq data and (3) identification and analysis of methylguanosine-capped and polyadenylated sRNAs (CPA-sRNAs). This species of small RNA is particularly interesting in Magnaporthe oryzae, as they map to transcription start and end sites of protein-coding genes. While we do not provide specific command lines for scripts, we provide a general framework for steps needed to carry out all three types of analyses, including relevant references, websites and free online tools. Screenshots are provided from our own customized interface using M. oryzae as an example, to assist the reader in visualizing many of the steps.
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http://dx.doi.org/10.1007/978-1-4939-8724-5_5 | DOI Listing |
Med Klin Intensivmed Notfmed
January 2025
Interdisciplinary Medical Intensive Care, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Straße 55, 79106, Freiburg, Germany.
Background: Venovenous extracorporeal membrane oxygenation (VV ECMO) is an established support option for patients with very severe respiratory failure and played an important role during the coronavirus disease 2019 (COVID-19) pandemic. Bacteria and fungi can lead to severe infectious complications in critically ill patients. The aim of this study was to describe the microbiological spectrum of bacteria and fungi detected in patients with COVID-19-associated respiratory failure supported with VV ECMO in our center.
View Article and Find Full Text PDFMicrob Biotechnol
January 2025
Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China.
Ascomycetes fungi are often prone to degeneration. Agricultural production of the prized ascomycete mushroom Morchella importuna (black morel) typically suffers from reduced yield and malformed ascocarps owing to culture degeneration. This study compared M.
View Article and Find Full Text PDFEnviron Microbiol
February 2025
Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Braga, Portugal.
Wine industry has faced pressure to innovate its products. Saccharomyces cerevisiae has been the traditional yeast for producing alcoholic beverages, but interest has shifted from the conventional S. cerevisiae to non-Saccharomyces yeasts for their biotechnological potential.
View Article and Find Full Text PDFColorectal Dis
February 2025
Department of Infectious Diseases, Hospital Universitari Parc Taulí, Sabadell, Spain.
Aim: Oral antibiotic prophylaxis (OAP) lowers rates of surgical site infection (SSI) and may aid anastomotic healing in colorectal surgery. The aim of this study was to analyse the understudied impact of OAP on SSI microbiology after colorectal surgery.
Method: A post hoc analysis was performed on a previous prospective, multicentre study of elective colorectal surgery.
Phytochem Anal
January 2025
Departamento de Productos Naturales, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior, Ciudad de México, Mexico.
Introduction: Antimicrobial resistance is a global public health problem that requires the development of new bioactive compounds. In this context, metabolomic analyses can expedite the research of fungal metabolites as a valuable resource.
Objectives: To investigate the metabolic profiles and isolate antibacterial compounds from micromycetes associated with Mexican cloud forest ants by utilizing network analysis of their chemical and bioactivity data.
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