TY  - JOUR
A1  - Nowak, Jacqueline
A1  - Gennermann, Kristin
A1  - Persson, Staffan
A1  - Nikoloski, Zoran
T1  - CytoSeg 2.0
BT  - automated extraction of actin filaments
JF  - Bioinformatics
N2  - Motivation:
Actin filaments (AFs) are dynamic structures that substantially change their organization over time. The dynamic behavior and the relatively low signal-to-noise ratio during live-cell imaging have rendered the quantification of the actin organization a difficult task. 

Results:
We developed an automated image-based framework that extracts AFs from fluorescence microscopy images and represents them as networks, which are automatically analyzed to identify and compare biologically relevant features. Although the source code is freely available, we have now implemented the framework into a graphical user interface that can be installed as a Fiji plugin, thus enabling easy access by the research community.
Y1  - 2020
U6  - https://doi.org/10.1093/bioinformatics/btaa035
SN  - 1367-4803
SN  - 1460-2059
VL  - 36
IS  - 9
SP  - 2950
EP  - 2951
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Küken, Anika
A1  - Gennermann, Kristin
A1  - Nikoloski, Zoran
T1  - Characterization of maximal enzyme catalytic rates in central metabolism of Arabidopsis thaliana
JF  - The plant journal
N2  - Availability of plant-specific enzyme kinetic data is scarce, limiting the predictive power of metabolic models and precluding identification of genetic factors of enzyme properties. Enzyme kinetic data are measuredin vitro, often under non-physiological conditions, and conclusions elicited from modeling warrant caution. Here we estimate maximalin vivocatalytic rates for 168 plant enzymes, including photosystems I and II, cytochrome-b6f complex, ATP-citrate synthase, sucrose-phosphate synthase as well as enzymes from amino acid synthesis with previously undocumented enzyme kinetic data in BRENDA. The estimations are obtained by integrating condition-specific quantitative proteomics data, maximal rates of selected enzymes, growth measurements fromArabidopsis thalianarosette with and fluxes through canonical pathways in a constraint-based model of leaf metabolism. In comparison to findings inEscherichia coli, we demonstrate weaker concordance between the plant-specificin vitroandin vivoenzyme catalytic rates due to a low degree of enzyme saturation. This is supported by the finding that concentrations of nicotinamide adenine dinucleotide (phosphate), adenosine triphosphate and uridine triphosphate, calculated based on our maximalin vivocatalytic rates, and available quantitative metabolomics data are below reportedKMvalues and, therefore, indicate undersaturation of respective enzymes. Our findings show that genome-wide profiling of enzyme kinetic properties is feasible in plants, paving the way for understanding resource allocation.
KW  - Arabidopsis thaliana
KW  - constraint-based modeling
KW  - enzyme catalytic rates
KW  - kinetic parameter
KW  - metabolic network
KW  - turnover number
Y1  - 2020
U6  - https://doi.org/10.1111/tpj.14890
SN  - 0960-7412
SN  - 1365-313X
VL  - 103
IS  - 6
SP  - 2168
EP  - 2177
PB  - Wiley
CY  - Oxford
ER  -