@article{BanksNishiyamaHasebeetal.2011,
  author    = {Banks, Jo Ann and Nishiyama, Tomoaki and Hasebe, Mitsuyasu and Bowman, John L. and Gribskov, Michael and dePamphilis, Claude and Albert, Victor A. and Aono, Naoki and Aoyama, Tsuyoshi and Ambrose, Barbara A. and Ashton, Neil W. and Axtell, Michael J. and Barker, Elizabeth and Barker, Michael S. and Bennetzen, Jeffrey L. and Bonawitz, Nicholas D. and Chapple, Clint and Cheng, Chaoyang and Correa, Luiz Gustavo Guedes and Dacre, Michael and DeBarry, Jeremy and Dreyer, Ingo and Elias, Marek and Engstrom, Eric M. and Estelle, Mark and Feng, Liang and Finet, Cedric and Floyd, Sandra K. and Frommer, Wolf B. and Fujita, Tomomichi and Gramzow, Lydia and Gutensohn, Michael and Harholt, Jesper and Hattori, Mitsuru and Heyl, Alexander and Hirai, Tadayoshi and Hiwatashi, Yuji and Ishikawa, Masaki and Iwata, Mineko and Karol, Kenneth G. and Koehler, Barbara and Kolukisaoglu, Uener and Kubo, Minoru and Kurata, Tetsuya and Lalonde, Sylvie and Li, Kejie and Li, Ying and Litt, Amy and Lyons, Eric and Manning, Gerard and Maruyama, Takeshi and Michael, Todd P. and Mikami, Koji and Miyazaki, Saori and Morinaga, Shin-ichi and Murata, Takashi and M{\"u}ller-R{\"o}ber, Bernd and Nelson, David R. and Obara, Mari and Oguri, Yasuko and Olmstead, Richard G. and Onodera, Naoko and Petersen, Bent Larsen and Pils, Birgit and Prigge, Michael and Rensing, Stefan A. and Mauricio Riano-Pachon, Diego and Roberts, Alison W. and Sato, Yoshikatsu and Scheller, Henrik Vibe and Schulz, Burkhard and Schulz, Christian and Shakirov, Eugene V. and Shibagaki, Nakako and Shinohara, Naoki and Shippen, Dorothy E. and Sorensen, Iben and Sotooka, Ryo and Sugimoto, Nagisa and Sugita, Mamoru and Sumikawa, Naomi and Tanurdzic, Milos and Theissen, Guenter and Ulvskov, Peter and Wakazuki, Sachiko and Weng, Jing-Ke and Willats, William W. G. T. and Wipf, Daniel and Wolf, Paul G. and Yang, Lixing and Zimmer, Andreas D. and Zhu, Qihui and Mitros, Therese and Hellsten, Uffe and Loque, Dominique and Otillar, Robert and Salamov, Asaf and Schmutz, Jeremy and Shapiro, Harris and Lindquist, Erika and Lucas, Susan and Rokhsar, Daniel and Grigoriev, Igor V.},
  title     = {The selaginella genome identifies genetic changes associated with the evolution of vascular plants},
  series = {Science},
  volume    = {332},
  journal   = {Science},
  number    = {6032},
  publisher = {American Assoc. for the Advancement of Science},
  address   = {Washington},
  issn      = {0036-8075},
  doi       = {10.1126/science.1203810},
  pages     = {960 -- 963},
  year      = {2011},
  abstract  = {Vascular plants appeared similar to 410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.},
  language  = {en}
}
@article{ToySutherlandTownendetal.2017,
  author    = {Toy, Virginia Gail and Sutherland, Rupert and Townend, John and Allen, Michael J. and Becroft, Leeza and Boles, Austin and Boulton, Carolyn and Carpenter, Brett and Cooper, Alan and Cox, Simon C. and Daube, Christopher and Faulkner, D. R. and Halfpenny, Angela and Kato, Naoki and Keys, Stephen and Kirilova, Martina and Kometani, Yusuke and Little, Timothy and Mariani, Elisabetta and Melosh, Benjamin and Menzies, Catriona D. and Morales, Luiz and Morgan, Chance and Mori, Hiroshi and Niemeijer, Andre and Norris, Richard and Prior, David and Sauer, Katrina and Schleicher, Anja Maria and Shigematsu, Norio and Teagle, Damon A. H. and Tobin, Harold and Valdez, Robert and Williams, Jack and Yeo, Samantha and Baratin, Laura-May and Barth, Nicolas and Benson, Adrian and Boese, Carolin and C{\´e}l{\´e}rier, Bernard and Chamberlain, Calum J. and Conze, Ronald and Coussens, Jamie and Craw, Lisa and Doan, Mai-Linh and Eccles, Jennifer and Grieve, Jason and Grochowski, Julia and Gulley, Anton and Howarth, Jamie and Jacobs, Katrina and Janku-Capova, Lucie and Jeppson, Tamara and Langridge, Robert and Mallyon, Deirdre and Marx, Ray and Massiot, C{\´e}cile and Mathewson, Loren and Moore, Josephine and Nishikawa, Osamu and Pooley, Brent and Pyne, Alex and Savage, Martha K. and Schmitt, Doug and Taylor-Offord, Sam and Upton, Phaedra and Weaver, Konrad C. and Wiersberg, Thomas and Zimmer, Martin},
  title     = {Bedrock geology of DFDP-2B, central Alpine Fault, New Zealand},
  series = {New Zealand journal of geology and geophysics : an international journal of the geoscience of New Zealand, the Pacific Rim, and Antarctica ; NZJG},
  volume    = {60},
  journal   = {New Zealand journal of geology and geophysics : an international journal of the geoscience of New Zealand, the Pacific Rim, and Antarctica ; NZJG},
  number    = {4},
  publisher = {Taylor \& Francis},
  address   = {Abingdon},
  organization    = {DFDP-2 Sci Team},
  issn      = {0028-8306},
  doi       = {10.1080/00288306.2017.1375533},
  pages     = {497 -- 518},
  year      = {2017},
  abstract  = {During the second phase of the Alpine Fault, Deep Fault Drilling Project (DFDP) in the Whataroa River, South Westland, New Zealand, bedrock was encountered in the DFDP-2B borehole from 238.5-893.2 m Measured Depth (MD). Continuous sampling and meso- to microscale characterisation of whole rock cuttings established that, in sequence, the borehole sampled amphibolite facies, Torlesse Composite Terrane-derived schists, protomylonites and mylonites, terminating 200-400 m above an Alpine Fault Principal Slip Zone (PSZ) with a maximum dip of 62°. The most diagnostic structural features of increasing PSZ proximity were the occurrence of shear bands and reduction in mean quartz grain sizes. A change in composition to greater mica:quartz + feldspar, most markedly below c. 700 m MD, is inferred to result from either heterogeneous sampling or a change in lithology related to alteration. Major oxide variations suggest the fault-proximal Alpine Fault alteration zone, as previously defined in DFDP-1 core, was not sampled.},
  language  = {en}
}
@article{ArendZimmerXuetal.2023,
  author    = {Arend, Marius and Zimmer, David and Xu, Rudan and Sommer, Frederik and M{\"u}hlhaus, Timo and Nikoloski, Zoran},
  title     = {Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scale},
  series = {Nature Communications},
  volume    = {14},
  journal   = {Nature Communications},
  number    = {1},
  publisher = {Springer Nature},
  address   = {London},
  issn      = {2041-1723},
  doi       = {10.1038/s41467-023-40498-1},
  pages     = {9},
  year      = {2023},
  abstract  = {Metabolic engineering of microalgae offers a promising solution for sustainable biofuel production, and rational design of engineering strategies can be improved by employing metabolic models that integrate enzyme turnover numbers. However, the coverage of turnover numbers for Chlamydomonas reinhardtii, a model eukaryotic microalga accessible to metabolic engineering, is 17-fold smaller compared to the heterotrophic cell factory Saccharomyces cerevisiae. Here we generate quantitative protein abundance data of Chlamydomonas covering 2337 to 3708 proteins in various growth conditions to estimate in vivo maximum apparent turnover numbers. Using constrained-based modeling we provide proxies for in vivo turnover numbers of 568 reactions, representing a 10-fold increase over the in vitro data for Chlamydomonas. Integration of the in vivo estimates instead of in vitro values in a metabolic model of Chlamydomonas improved the accuracy of enzyme usage predictions. Our results help in extending the knowledge on uncharacterized enzymes and improve biotechnological applications of Chlamydomonas.},
  language  = {en}
}