TY  - JOUR
A1  - Banks, Jo Ann
A1  - Nishiyama, Tomoaki
A1  - Hasebe, Mitsuyasu
A1  - Bowman, John L.
A1  - Gribskov, Michael
A1  - dePamphilis, Claude
A1  - Albert, Victor A.
A1  - Aono, Naoki
A1  - Aoyama, Tsuyoshi
A1  - Ambrose, Barbara A.
A1  - Ashton, Neil W.
A1  - Axtell, Michael J.
A1  - Barker, Elizabeth
A1  - Barker, Michael S.
A1  - Bennetzen, Jeffrey L.
A1  - Bonawitz, Nicholas D.
A1  - Chapple, Clint
A1  - Cheng, Chaoyang
A1  - Correa, Luiz Gustavo Guedes
A1  - Dacre, Michael
A1  - DeBarry, Jeremy
A1  - Dreyer, Ingo
A1  - Elias, Marek
A1  - Engstrom, Eric M.
A1  - Estelle, Mark
A1  - Feng, Liang
A1  - Finet, Cedric
A1  - Floyd, Sandra K.
A1  - Frommer, Wolf B.
A1  - Fujita, Tomomichi
A1  - Gramzow, Lydia
A1  - Gutensohn, Michael
A1  - Harholt, Jesper
A1  - Hattori, Mitsuru
A1  - Heyl, Alexander
A1  - Hirai, Tadayoshi
A1  - Hiwatashi, Yuji
A1  - Ishikawa, Masaki
A1  - Iwata, Mineko
A1  - Karol, Kenneth G.
A1  - Koehler, Barbara
A1  - Kolukisaoglu, Uener
A1  - Kubo, Minoru
A1  - Kurata, Tetsuya
A1  - Lalonde, Sylvie
A1  - Li, Kejie
A1  - Li, Ying
A1  - Litt, Amy
A1  - Lyons, Eric
A1  - Manning, Gerard
A1  - Maruyama, Takeshi
A1  - Michael, Todd P.
A1  - Mikami, Koji
A1  - Miyazaki, Saori
A1  - Morinaga, Shin-ichi
A1  - Murata, Takashi
A1  - Müller-Röber, Bernd
A1  - Nelson, David R.
A1  - Obara, Mari
A1  - Oguri, Yasuko
A1  - Olmstead, Richard G.
A1  - Onodera, Naoko
A1  - Petersen, Bent Larsen
A1  - Pils, Birgit
A1  - Prigge, Michael
A1  - Rensing, Stefan A.
A1  - Mauricio Riano-Pachon, Diego
A1  - Roberts, Alison W.
A1  - Sato, Yoshikatsu
A1  - Scheller, Henrik Vibe
A1  - Schulz, Burkhard
A1  - Schulz, Christian
A1  - Shakirov, Eugene V.
A1  - Shibagaki, Nakako
A1  - Shinohara, Naoki
A1  - Shippen, Dorothy E.
A1  - Sorensen, Iben
A1  - Sotooka, Ryo
A1  - Sugimoto, Nagisa
A1  - Sugita, Mamoru
A1  - Sumikawa, Naomi
A1  - Tanurdzic, Milos
A1  - Theissen, Guenter
A1  - Ulvskov, Peter
A1  - Wakazuki, Sachiko
A1  - Weng, Jing-Ke
A1  - Willats, William W. G. T.
A1  - Wipf, Daniel
A1  - Wolf, Paul G.
A1  - Yang, Lixing
A1  - Zimmer, Andreas D.
A1  - Zhu, Qihui
A1  - Mitros, Therese
A1  - Hellsten, Uffe
A1  - Loque, Dominique
A1  - Otillar, Robert
A1  - Salamov, Asaf
A1  - Schmutz, Jeremy
A1  - Shapiro, Harris
A1  - Lindquist, Erika
A1  - Lucas, Susan
A1  - Rokhsar, Daniel
A1  - Grigoriev, Igor V.
T1  - The selaginella genome identifies genetic changes associated with the evolution of vascular plants
JF  - Science
N2  - 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.
Y1  - 2011
U6  - https://doi.org/10.1126/science.1203810
SN  - 0036-8075
VL  - 332
IS  - 6032
SP  - 960
EP  - 963
PB  - American Assoc. for the Advancement of Science
CY  - Washington
ER  - 
TY  - JOUR
A1  - Toy, Virginia Gail
A1  - Sutherland, Rupert
A1  - Townend, John
A1  - Allen, Michael J.
A1  - Becroft, Leeza
A1  - Boles, Austin
A1  - Boulton, Carolyn
A1  - Carpenter, Brett
A1  - Cooper, Alan
A1  - Cox, Simon C.
A1  - Daube, Christopher
A1  - Faulkner, D. R.
A1  - Halfpenny, Angela
A1  - Kato, Naoki
A1  - Keys, Stephen
A1  - Kirilova, Martina
A1  - Kometani, Yusuke
A1  - Little, Timothy
A1  - Mariani, Elisabetta
A1  - Melosh, Benjamin
A1  - Menzies, Catriona D.
A1  - Morales, Luiz
A1  - Morgan, Chance
A1  - Mori, Hiroshi
A1  - Niemeijer, Andre
A1  - Norris, Richard
A1  - Prior, David
A1  - Sauer, Katrina
A1  - Schleicher, Anja Maria
A1  - Shigematsu, Norio
A1  - Teagle, Damon A. H.
A1  - Tobin, Harold
A1  - Valdez, Robert
A1  - Williams, Jack
A1  - Yeo, Samantha
A1  - Baratin, Laura-May
A1  - Barth, Nicolas
A1  - Benson, Adrian
A1  - Boese, Carolin
A1  - Célérier, Bernard
A1  - Chamberlain, Calum J.
A1  - Conze, Ronald
A1  - Coussens, Jamie
A1  - Craw, Lisa
A1  - Doan, Mai-Linh
A1  - Eccles, Jennifer
A1  - Grieve, Jason
A1  - Grochowski, Julia
A1  - Gulley, Anton
A1  - Howarth, Jamie
A1  - Jacobs, Katrina
A1  - Janku-Capova, Lucie
A1  - Jeppson, Tamara
A1  - Langridge, Robert
A1  - Mallyon, Deirdre
A1  - Marx, Ray
A1  - Massiot, Cécile
A1  - Mathewson, Loren
A1  - Moore, Josephine
A1  - Nishikawa, Osamu
A1  - Pooley, Brent
A1  - Pyne, Alex
A1  - Savage, Martha K.
A1  - Schmitt, Doug
A1  - Taylor-Offord, Sam
A1  - Upton, Phaedra
A1  - Weaver, Konrad C.
A1  - Wiersberg, Thomas
A1  - Zimmer, Martin
T1  - Bedrock geology of DFDP-2B, central Alpine Fault, New Zealand
JF  - New Zealand journal of geology and geophysics : an international journal of the geoscience of New Zealand, the Pacific Rim, and Antarctica ; NZJG
N2  - 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.
KW  - Alpine Fault
KW  - New Zealand
KW  - scientific drilling
KW  - mylonite
KW  - cataclasite
Y1  - 2017
U6  - https://doi.org/10.1080/00288306.2017.1375533
SN  - 0028-8306
SN  - 1175-8791
VL  - 60
IS  - 4
SP  - 497
EP  - 518
PB  - Taylor & Francis
CY  - Abingdon
ER  - 
TY  - JOUR
A1  - Arend, Marius
A1  - Zimmer, David
A1  - Xu, Rudan
A1  - Sommer, Frederik
A1  - Mühlhaus, Timo
A1  - Nikoloski, Zoran
T1  - Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scale
JF  - Nature Communications
N2  - 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.
KW  - Computational models
KW  - Enzymes
KW  - Proteomics
Y1  - 2023
U6  - https://doi.org/10.1038/s41467-023-40498-1
SN  - 2041-1723
VL  - 14
IS  - 1
PB  - Springer Nature
CY  - London
ER  -