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SUMMARY:The Methylome and Deep RNome in Clostridium: New Gadgets Uncover L
 arger Cellular Complexity
DTSTART:20141212T123000
DTSTAMP:20260427T225327Z
UID:969258cbde84a69faca60697756bc6c331915755446a4098723f35f6
CATEGORIES:Conferences - Seminars
DESCRIPTION:Prof. Eleftherios Terry Papoutsakis\, University of Delaware\,
  Newark\, DE (USA)\nBIOENGINEERING SEMINARAbstract:\nNew technologies now 
 enable a considerably more detailed picture of the state of nucleic acids 
 in organisms\, and notably of the DNA methylation and the deep\, strand-sp
 ecific RNome. Here we examined the methylome (state of DNA methylation) of
  Clostridium acetobutylicum and C. pasterianum under normal and\, for C. a
 cetobutylicum\, metabolite stress conditions. We also used Illumina-based 
 strand-specific RNAseq to probe the deep RNome of C. acetobutylicum under 
 both normal and stress conditions.\nSeveral strains of C. acetobutylicum a
 nd C. pasterianum were sequenced and assembled via Single Molecule Real-Ti
 me (SMRT\; PacBio) sequencing. The WT C. pasterianum type was assembled in
 to 2 contigs (4.4 Mb) and was compared to the previously published version
  of the same strain\, which exists in 37 contigs with a total length of 4.
 28 Mb. Mutations introduced to an evolved\, more tolerant to crude glycero
 l C. pasterianum strain were identified by sequence comparison to the WT. 
 DNA methylation patterns identified with SMRT sequencing were used to aid 
 in optimization of transformation efficiency of plasmid DNA. The DNA methy
 lome of C. acetobutylicum under normal versus metabolite stress conditions
  was also compared aiming to understand the impact of stress on DNA methyl
 ation and if this is possibly related to cell survival and gene expression
 . Strand-specific RNAseq was employed to explore the complex transcriptome
  of these two organisms\, with emphasis on identifying strand-specific exp
 ression of small RNAs (both cis and trans)\, unknown genes\, and also tran
 scriptional start sites to probe the impact of culture conditions on the r
 ich RNome of these organisms. The results demonstrate a much richer RNome 
 that could anticipated\, to the point in fact that the expected RNome base
 d on the genome is only a small fraction of the experimentally observed st
 rand-specific RNome. The information that can be extracted from such data 
 leads to new ways to solve old problems\, and significantly provides a muc
 h deeper understanding of the inner workings of the cells.Bio:\nDr. Papout
 sakis comes to UD from Northwestern University\, where he served as Walter
  P. Murphy Professor of Chemical and Biological Engineering and also was a
  member of the Lurie Comprehensive Cancer Center of the Northwestern Unive
 rsity Medical School. Before that\, he was a member of the Rice University
  faculty.\nHis research focuses on areas of systems biology\, metabolic en
 gineering\, experimental and computational genomics with applications in s
 tem-cell biology and prokaryotic biology for the production of biofuels an
 d chemicals from biomass.\nA fellow of the American Academy of Microbiolog
 y and the American Association for the Advancement of Science and a foundi
 ng fellow of the American Institute of Medical and Biological Engineers\, 
 Papoutsakis also has received several awards\, including the Amgen Biochem
 ical Engineering Award and the Merck Cell Culture Engineering Award\, both
  from the from Engineering Conferences International\; the Alpha Chi Sigma
  Award and the Food\, Pharmaceutical and Bioengineering Award\, both from 
 the American Institute of Chemical Engineers\; and the Marvin Johnson Awar
 d and the Van Lanen Award\, both from the Biochemical Technology Division 
 of the American Chemical Society. Papoutsakis has published extensively in
  his field and served as editor-in-chief of Biotechnology and Bioengineeri
 ng. He also serves on the advisory boards of four journals in the field of
  biotechnology and tissue engineering\, and on the organizing committees o
 r advisory boards of many international meetings. He has authored several 
 issued and pending patents. He has served or serves on the Scientific Advi
 sory Boards (SAB) of four biotechnology companies. He consults regularly a
 nd offers expert witness services in the field of biotechnology\, and biom
 edical sciences more broadly.\nA graduate of the National Technical Univer
 sity of Athens\, Greece\, Papoutsakis received his Master's and Doctoral d
 egrees from Purdue University.
LOCATION:SV1717a http://map.epfl.ch/?room=sv1717a
STATUS:CONFIRMED
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