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- ItemGenome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation(San Francisco, CA : Public Library of Science (PLoS), 2013) Winck, F.V.; Arvidsson, S.; Riaño-Pachón, D.M.; Hempe, S.; Koseska, A.; Nikoloski, Z.; Gomez, D.A.U.; Rupprecht, J.; Mueller-Roeber, B.The unicellular green alga Chlamydomonas reinhardtii is a long-established model organism for studies on photosynthesis and carbon metabolism-related physiology. Under conditions of air-level carbon dioxide concentration [CO 2], a carbon concentrating mechanism (CCM) is induced to facilitate cellular carbon uptake. CCM increases the availability of carbon dioxide at the site of cellular carbon fixation. To improve our understanding of the transcriptional control of the CCM, we employed FAIRE-seq (formaldehyde-assisted Isolation of Regulatory Elements, followed by deep sequencing) to determine nucleosome-depleted chromatin regions of algal cells subjected to carbon deprivation. Our FAIRE data recapitulated the positions of known regulatory elements in the promoter of the periplasmic carbonic anhydrase (Cah1) gene, which is upregulated during CCM induction, and revealed new candidate regulatory elements at a genome-wide scale. In addition, time series expression patterns of 130 transcription factor (TF) and transcription regulator (TR) genes were obtained for cells cultured under photoautotrophic condition and subjected to a shift from high to low [CO2]. Groups of co-expressed genes were identified and a putative directed gene-regulatory network underlying the CCM was reconstructed from the gene expression data using the recently developed IOTA (inner composition alignment) method. Among the candidate regulatory genes, two members of the MYB-related TF family, Lcr1 (Low-CO2 response regulator 1) and Lcr2 (Low-CO2 response regulator 2 ), may play an important role in down-regulating the expression of a particular set of TF and TR genes in response to low [CO2]. The results obtained provide new insights into the transcriptional control of the CCM and revealed more than 60 new candidate regulatory genes. Deep sequencing of nucleosome-depleted genomic regions indicated the presence of new, previously unknown regulatory elements in the C. reinhardtii genome. Our work can serve as a basis for future functional studies of transcriptional regulator genes and genomic regulatory elements in Chlamydomonas.
- ItemImpact of the precursor chemistry and process conditions on the cell-to-cell variability in 1T-1R based HfO2 RRAM devices(London : Nature Publishing Group, 2018) Grossi, A.; Perez, E.; Zambelli, C.; Olivo, P.; Miranda, E.; Roelofs, R.; Woodruff, J.; Raisanen, P.; Li, W.; Givens, M.; Costina, I.; Schubert, M.A.; Wenger, C.The Resistive RAM (RRAM) technology is currently in a level of maturity that calls for its integration into CMOS compatible memory arrays. This CMOS integration requires a perfect understanding of the cells performance and reliability in relation to the deposition processes used for their manufacturing. In this paper, the impact of the precursor chemistries and process conditions on the performance of HfO2 based memristive cells is studied. An extensive characterization of HfO2 based 1T1R cells, a comparison of the cell-to-cell variability, and reliability study is performed. The cells’ behaviors during forming, set, and reset operations are monitored in order to relate their features to conductive filament properties and process-induced variability of the switching parameters. The modeling of the high resistance state (HRS) is performed by applying the Quantum-Point Contact model to assess the link between the deposition condition and the precursor chemistry with the resulting physical cells characteristics.