Browsing by Subject "DATABASES"

Sort by: Order: Results:

Now showing items 1-4 of 4
  • Marchet, Camille; Boucher, Christina; Puglisi, Simon J.; Medvedev, Paul; Salson, Mikael; Chikhi, Rayan (2021)
    High-throughput sequencing data sets are usually deposited in public repositories (e.g., the European Nucleotide Archive) to ensure reproducibility. As the amount of data has reached petabyte scale, repositories do not allow one to perform online sequence searches, yet, such a feature would be highly useful to investigators. Toward this goal, in the last few years several computational approaches have been introduced to index and query large collections of data sets. Here, we propose an accessible survey of these approaches, which are generally based on representing data sets as sets of k-mers. We review their properties, introduce a classification, and present their general intuition. We summarize their performance and highlight their current strengths and limitations.
  • van der Ark, Kees C. H.; Aalvink, Steven; Suarez-Diez, Maria; Schaap, Peter J.; de Vos, Willem M.; Belzer, Clara (2018)
    The abundance of the human intestinal symbiont Akkermansia muciniphila has found to be inversely correlated with several diseases, including metabolic syndrome and obesity. A.muciniphila is known to use mucin as sole carbon and nitrogen source. To study the physiology and the potential for therapeutic applications of this bacterium, we designed a defined minimal medium. The composition of the medium was based on the genome-scale metabolic model of A.muciniphila and the composition of mucin. Our results indicate that A.muciniphila does not code for GlmS, the enzyme that mediates the conversion of fructose-6-phosphate (Fru6P) to glucosamine-6-phosphate (GlcN6P), which is essential in peptidoglycan formation. The only annotated enzyme that could mediate this conversion is Amuc-NagB on locus Amuc_1822. We found that Amuc-NagB was unable to form GlcN6P from Fru6P at physiological conditions, while it efficiently catalyzed the reverse reaction. To overcome this inability, N-acetylglucosamine needs to be present in the medium for A.muciniphila growth. With these findings, the genome-scale metabolic model was updated and used to accurately predict growth of A.muciniphila on synthetic media. The finding that A.muciniphila has a necessity for GlcNAc, which is present in mucin further prompts the adaptation to its mucosal niche.
  • Knaappila, Noora; Marttunen, Mauri; Fröjd, Sari; Lindberg, Nina; Kaltiala-Heino, Riittakerttu (2019)
  • Swertz, Morris A.; Dijkstra, Martijn; Adamusiak, Tomasz; van der Velde, Joeri K.; Kanterakis, Alexandros; Roos, Erik T.; Lops, Joris; Thorisson, Gudmundur A.; Arends, Danny; Byelas, George; Muilu, Juha; Brookes, Anthony J.; de Brock, Engbert O.; Jansen, Ritsert C.; Parkinson, Helen (2010)