Gen om e d iver si ty

Partner Junior Research Group starting in Juli 2008. Several 
state-of-the-art methods for analysis and modelling of meta-
bolism have been established and productively applied. the 
main method is steady-state metabolic flux analysis, in which 
computational models of plant metabolism are enriched by 
stable isotope labelling data obtained in the lab. this method 
has been applied to investigate metabolic processes taking 
place at the filling stage in legume seeds, especially pea (Pisum 
sativum) and barrel medic (Medicago truncatula), as well as  

147
2013
b
aker
,  S.M., c.h. P
oskar
, F. S
chreiber
 & b.h. J
unker
: an improved 
constraint filtering technique for inferring hidden states 
and parameters of a biological model. bioinformatics 29 
(2013) 1052-1059.
G
rafahrend
-b
elau
, e., a. J
unker
, a. e
schenröder
, J. M
üller
, F. S
chreiber
 
& b.h. J
unker
: Multiscale metabolic modeling: dynamic flux 
balance analysis on a whole plant scale. Plant Physiol. 163 
(2013) 637-647.
M
üller
, J., a. e
schenröder
, o. c
hristen
, b.h. J
unker
 & F. S
chreiber
: Pro-
net-cn model: a dynamic and hierarchical process network 
that couples photosynthesis, primary carbon metabolism 
and effects of leaf nitrogen status. Proc. 2012 ieee 4
th
 int. 
Symp. Plant Growth Modeling, Simulation, Visualization 
and applications – PMa (2013) 289-296.
Books and Book Chapters
2012
G
rafahrend
-b
elau
,  e., b.h. J
unker
 & F. S
chreiber
: Plant metabolic 
path ways: database and pipeline for stoichiometric analy-
sis. in: a
grawal
, G.k. & R. R
akwal
 (eds.): Seed development: 
omics technologies toward improvement of seed quality 
and crop yield. Springer, dordrecht, the netherlands (2012) 
345-366.
J
unker
,  a. & b.h. J
unker
: Synthetic gene networks in plant sys-
tems. in: W
eber
,  w. & M. F
ussenegger
 (eds.): Synthetic gene 
networks: Methods and Protocols. Meth. Mol. biol. 813. hu-
mana Press, new York (2012) 343-358.
k
rach
, c., e. G
rafahrend
-b
elau
, h. P
oskar
, k. S
challau
, F. S
chreiber
 & 
b.h. J
unker
: using systems approaches to analyze metabolic 
networks involved in storage reserve synthesis in develop-
ing seeds. in: a
grawal
, G.k. & R. R
akwal
 (eds.): Seed develop-
ment: omics technologies toward improvement of seed 
quality and crop yield. Springer, dordrecht, the nether-
lands (2012) 387-406.
2013
J
unker
,  b.h. & S. k
empa
: isotope-based, non-steady state flux 
analysis. in: d
ubitzky
, W., o. W
olkenhauer
, k.-h. c
ho
 & h. Y
o
-
kota
 (eds.): encyclopedia of Systems biology. Springer 
Science+business Media, LLc (2013) 1056-1057.
Other Papers
2013
F
ranke
,  M., J. h
üge
, P. t
ablack
 & b.h. J
unker
: Messung von intra-
zellulären Stoffflüssen in Pflanzen. biospektrum 19 (2013) 
690-693.
due to the highly complex and laborious nature of steady-state 
metabolic flux analysis, in the past the method has been applied 
to a small number of genotypes or treatments (usually not more 
than 3 per study). We have significantly increased the through-
put of the method by using lab automation, simplifying the la-
boratory protocols, and automating the computational pipeline 
from data extraction to flux modelling. this increased through-
put enabled us to analyze metabolic fluxes in a population of 50 
barley introgression lines . Fluxes were then compared to meta-
bolic profiles that were additionally measured. this large data 
set is currently being prepared for publication. 
Several stoichiometric and kinetic models have been set up for 
seed metabolism in different species (k. Schallau, S. Weber, k. 
Lotz, S.M. baker), covering primary metabolism of the seeds. 
these models are constantly filled by experimental data, which 
are derived from metabolite and enzyme measurements (n. 
Schäfer, F. kellner, V. Peter). For pea seeds, we have set up a non-
aqueous technique to analyze metabolites and enzymes at a 
sub-cellular resolution (t. Liiving). For kinetic modelling, para-
meters that could not be measured may be estimated by a new 
computational pipeline for parameter identifiability analysis 
and parameter estimation with an improved algorithm tailored 
for biochemical data (S.M. baker). With the help of the kinetic 
models, targets for metabolic engineering can be predicted to 
improve seed composition. We have generated several trans-
genic pea lines to verify the predicted strategies. these lines are 
currently analyzed.
Since January 2013 björn Junker holds a permanent profes-
sorship at the Martin Luther university in halle. the research 
group continued operation in Gatersleben until June 2013. the 
projects that could not be finished at the iPk will be pursued at 
university halle-Wittenberg.
Publications
Peer Reviewed Papers
2012
h
uege
,  J., c.h. P
oskar
, M. F
ranke
 & b.h. J
unker
: towards high 
throughput metabolic flux analysis in plants. Mol. bioSyst. 
8 (2012) 2466-2469.
P
oskar
, c.h., J. h
uege
, c. k
rach
, M. F
ranke
, Y. S
hachar
-h
ill
 & b.h. J
un
-
ker
: iMS2Flux – a high-throughput processing tool for stable 
isotope labeled mass spectrometric data used for metabo-
lic flux analysis. bMc bioinformatics 13 (2012) 295.
R
ohn
, h., a. h
artmann
, a. J
unker
, b.h. J
unker
 & F. S
chreiber
: FluxMap: 
a Vanted add-on for the visual exploration of flux distribu-
tions in biological networks. bMc Syst. biol. 6 (2012) 33.
S
chreiber
, F., c. c
olmsee
, t. c
zauderna
, e. G
rafahrend
-b
elau
, a. h
art
-
mann
, a. J
unker
, b.h. J
unker
, M. k
lapperstück
, u. S
cholz
 & S. W
eise
: 
Metacrop 2.0: managing and exploring information about 
crop plant metabolism. nucleic acids Res. 40 (2012) d1173-
d1177.

Abteilung Physiologie und Zellbiologie/
Department of Physiology and Cell Biology
148
PhD and Diploma Theses
2012
b
aker
, S.M.: a parameter estimation framework for kinetic mo-
dels of biological systems. (Phd thesis) Martin-Luther-uni-
versität halle-Wittenberg, institut für informatik der natur-
wissenschaftlichen Fakultät iii, halle/S. (2012) 150 pp.
k
umpf
,  a.: homologe Gene des Brittle1- transporters in Pisum 
sativum. (bachelor thesis) hochschule anhalt (Fh), köthen 
(2012) 68 pp. (hochschulbetreuer aus dem iPk: Prof. G. kun-
ze, dr. u. Scholz).
2013
F
reier
,  L.: dynamic metabolic flux analysis (dMFa) applied to 
the calvin cycle of Nicotiana tabacum. (Master thesis) otto-
von-Guericke-universität Magdeburg, Magdeburg (2013) 
116 pp.
k
lepsch
, o.: bedeutung des Lichts im Metabolismus adP-Gluko-
se Pyrophosphorylase-defizienter erbsen (Pisum sativum) 
während der Samenentwicklung. (bachelor thesis) otto-
von-Guericke-universität Magdeburg, Magdeburg (2013) 
72 pp.
S
chumann
,  J.: der einfluss von alanin auf die berechnung von 
quantitativen Stoffwechselkarten in erbsen-embryos. 
(Master thesis) Martin-Luther-universität halle-Wittenberg, 
halle/S. (2013) 99 pp.
V
elten
,  S.: Methodische erweiterung der metabolischen Fluss-
analyse im steady state (ssMFa) zur Gewinnung von 
 
13
c-Markierungsinformationen aus löslichen Stoffwechsel-
intermediaten. (bachelor thesis) otto-von-Guericke-uni-
versität Magdeburg, Magdeburg (2013) 172 pp.

149
B. napus were analysed to design specific primers allowing the 
cloning of the complete set of bnniP isoforms. Sixteen out of 
27 expected isoforms were successfully cloned and their full-
length gene sequences determined. this information is used 
at the moment to determine the genomic sequence of BnNIPs 
with a specific focus on promoter regions which will be used 
for promoter-reporter-gene analysis. in parallel, we prepare a 
set of molecular tools and vectors which will be used for the 
analysis of the substrate specificity of bnniPs in planta, in the 
heterologous expression systems Saccharomyces cerevisiae and 
in Xenopus laevis oocytes, as well as for the determination of 
their subcellular localisation (in cooperation with the research 
group Structural cell biology).
to resolve the mostly unknown impact of the B nutritional 
status on gene regulation and metabolism, a transcript and 
metabolite profile of b-sufficient and b-deficient oilseed and A. 
thaliana plants will be generated in cooperation with the re-
search groups applied biochemistry and Molecular Plant nutri-
tion.
together with the group of Molecular Plant nutrition, we aim at 
identifying transcription factors (tF), which coordinate b trans-
port processes, perception and regulation. an elemental analy-
sis of a tF knockout collection of Arabidopsis was performed 
with plants grown on b-sufficient conditions. Six lines carrying 
insertions in to date non-characterized tFs possess either at 
least 25 % higher or lower b levels than the wild type. these 
measurements will be repeated and the role of individual tFs in 
b nutrition analysed (R. Giehl, b. Pommerrenig).
to establish a screening platform for the selection of B-de-
ficiency tolerant European rapeseed genotypes, we estab-
lished two independent screening conditions which on the 
one hand allow a phenotypic description of the b efficiency of 
a given cultivar at the seedling stage in soil conditions and on 
the other hand the quantitative assessment of b efficiency via 
the evaluation of parameters describing the rapid root growth 
inhibition under b deficiency (Fig. 46 b). these assays were es-
tablished and assessed using european and asian rapeseed 
cultivars known to differ in b-efficiency. the Genebank depart-
ment at the iPk provided a highly valuable collection for such 
a screen. between the two most divergently behaving cultivars 
to be identified (with respect to their response to the b treat-
ment), a detailed qualitative comparison of b transport routes/
parameters and molecular b transport mechanisms will be per-
formed under different b regimes. this will allow to determine 
the qualitative and mechanistic B uptake and allocation dif-
ferences between B-efficient and -inefficient B. napus culti-
vars (G.P. bienert, b. Pommerrenig). 
Research Group: Metalloid-Transport
 (since 01.05.2013)
 
(emmy noether Group, dFG)
head:  dr. Gerd Patrick bienert
Scientists
Grant Positions
diehn, arvid (0,65 dFG, since 15.09.2013)
Pommerrenig, benjamin, dr. (dFG, since 01.10.2013)
Goals
the main objective of the research group “Metalloid transport” 
is to study the mechanisms regulating the boron (b) nutritional 
status in rapeseed and Arabidopsis and their implications for 
the development of boron-efficient genotypes.
Research Report
the dFG-funded emmy noether research group “Metalloid 
transport” was successfully established at the iPk. team mem-
bers have been recruited and the laboratory space was set up 
and equipped. the research group, which is now fully opera-
tional was initiated to study the mechanisms regulating the bo-
ron (b) nutritional status in rapeseed and Arabidopsis and their 
implications for the development of boron-efficient genotypes.
the project addresses the question of how b deficiency-sen-
sitive Brassica crop plants process and regulate their b status 
during vegetative and reproductive growth. in this context, the 
project aims at identifying the mode of action of B in mech-
anisms regulating the B status itself and uncovering those 
mechanisms contributing to B efficiency in different geno-
types. a detailed understanding of mechanisms controlling b 
uptake and allocation from the level of the whole plant down 
to the cellular level will be established. the above outlined 
work will expand the scope of the research in the “Molecular 
Plant nutrition” group and complement their research direc-
tion to generate a situation of mutual benefit. We focus on the 
identification of b deficiency-sensitive transport processes to 
and within highly b-demanding reproductive organs. a certain 
subgroup of nodulin26-like intrinsic Proteins (niPs) is essential 
for plant b uptake and distribution. the systematic focus on 
the  molecular and physiological characterization of Bras-
sica napus NIPs will clarify their role in the b response network 
in this plant species (a. diehn, b. Pommerrenig, see Fig. 46 a,  
p. 150). to this aim, and as the genomic sequence of B. napus is 
not publicly available yet, sequence information and eSt data 
from Arabidopsis thaliana, Brassica rapa, Brassica oleracea and 

Abteilung Physiologie und Zellbiologie/
Department of Physiology and Cell Biology
150
additionally, the following cooperations with other research 
groups within the iPk will be pursued: 
 
– Pollen embryogenesis, germination and elongation is high-
ly dependent on sufficient b supply of the reproductive or-
gans. together with the research group “Plant Reproductive 
biology” this phenomenon will be further elucidated. 
 
– b deficiency leads to morphological changes due to an 
impaired cell elongation and differentiation which will be 
analysed in cooperation with the research group “Structural 
cell biology”.
Publications
(All publications are based on work that has been carried out when 
Dr. Gerd Patrick Bienert was at the Institut des Sciences de la Vie
,
 
Université Catholique de Louvain in Louvain-la-Neuve/Belgium).
Peer Reviewed Papers
2013
b
ienert
, G.P., b. d
esguin
, F. c
haumont
 & P. h
ols
: channel-mediated 
lactic acid transport: a novel function for aquaglyceropor-
ins in bacteria. biochem. J. 454 (2013) 559-570.
Books and Book Chapters
2013
b
ienert
, G.P. & F. c
haumont
: Selenium and aquaporins. in: k
retsin
-
ger
, R.h., V.n. u
versky
 & e.a. P
ermyakov
 (eds.): encyclopedia of 
Metalloproteins. Springer, new York (2013) 1891-1893.
b
ienert
, G.P. & F. c
haumont
: boron and aquaporins. in: k
retsinger
, 
R.h., V.n. u
versky
 & e.a. P
ermyakov
 (eds.): encyclopedia of 
Metal loproteins. Springer, new York (2013) 291-294.
b
ienert
, G.P. & F. c
haumont
: arsenic and aquaporins. in: k
retsinger
,  
R.h., V.n. u
versky
 & e.a. P
ermyakov
 (eds.): encyclopedia of  
Metalloproteins. Springer, new York (2013) 101-106.
b
ienert
, G.P. & F. c
haumont
: Silicon and aquaporins. in: k
retsinger
, 
R.h., V.n. u
versky
 & e.a. P
ermyakov
 (eds.): encyclopedia of Met-
alloproteins. Springer, new York (2013) 1979-1982.
c
haumont
, F. & G.P. b
ienert
: aquaporins and transport of metal-
loids. in: k
retsinger
, R.h., V.n. u
versky
 & e.a. P
ermyakov
 (eds.): 
encyclopedia of Metalloproteins. Springer, new York (2013) 
92-94.
Fig. 46
Putative boron transporters and mechanisms regulating the boron nutritional 
status in Brassica napus.
A) Genome-wide sequence identification of aquaporin genes in the sequenced 
diploid genomes of Brassica oleracea and Brassica rapa, the genome donors 
of the tetraploid Brassica napus. these sequence information contribute to 
the identification of putative boron channel proteins (nodulin26-like intrinsic 
Proteins) in B. napus (niP, nodulin26-like intrinsic Protein; tiP, tonoplast intrinsic 
Protein; SiP, Small basic intrinsic Protein and PiP, Plasma membrane intrinsic 
Protein).
B)  a large number of cultivars of summer and winter-type oilseed rape were 
cultivated on boron-deficient soil substrate. Some of these cultivars showed 
almost no growth inhibition compared to boron-sufficient conditions and 
displayed no typical boron deficiency symptoms such as malformed leaves or 
the loss of the apical dominance. Genetic parameters as well as molecular and 
physiological mechanisms underlying the differences of the b-efficient and 
-inefficient B. napus cultivars will be determined (a. diehn, b. Pommerrenig).
boron (in form of boric acid) and arsenite (as) share the same 
proteineous niP-mediated transport pathways. to assess the 
consequences of this dual transport pathway, the so far un-
studied impact of the plant’s B nutritional status on the ac-
cumulation and distribution of As will be investigated. to 
this aim, publicly available Arabidopsis nip knockout mutants 
were collected to investigate the molecular and physiological 
responses of these mutant lines under varying metalloid treat-
ments. Furthermore, databases and publications were analysed 
aiming to identify Arabidopsis Wt accessions which either pos-
sess very low or very high b and as levels compared to “average 
accessions”. these publically available data will be confirmed 
and the molecular mechanisms underlying the differential 
metalloid acquisitions will be studied (G.P. bienert).

151
o
chsmann
, j., r. n
arang
 & h. k
nüpffer
. iPk Genebank and taxon-
omy image database. http://mansfeld.ipk-gatersleben.de/
imagedata/search_names-img.htm.
o
ppermann
, m.: iPk Malchow/Poel Wetterdaten – weather infor-
mation. http://apex.ipk-gatersleben.de/apex/f?p=271. 
o
ppermann
,  m.  &  j.  g
rässler
: iPk Gatersleben Wetterdaten – 
weather information. http://wetter.ipk-gatersleben.de/.
o
ppermann
, M. & h. k
nüpffer
. GbiS/i – Genebank information Sys-
tem of the iPk Gatersleben. http://gbis.ipk-gatersleben.de/.
p
istrick
, k., j. o
chsmann
 & r. n
arang
. herbarium iPk Gatersleben. 
http://mansfeld.ipk-gatersleben.de/herbarium/default.
htm.
R
ohn
,  h., a. J
unker
, a. h
artmann
, e. G
rafahrend
-b
elau
, h. t
reutler
,  
M. k
lapperstück
, t. c
zauderna
, c. k
lukas
 & F. S
chreiber
: Vanted 
2.0. http://www.vanted.org.
S
cholz
,  u., c. k
ünne
, M. L
ange
, h. M
iehe
 & t. F
unke
: cR-eSt: a re-
source for crop eSts. http://pgrc.ipk-gatersleben.de/cr-est.
S
chreiber
, F., c. c
olmsee
, t. c
zauderna
, e. G
rafahrend
-b
elau
, a. h
art
-
mann
, a. J
unker
, b.h. J
unker
, d. k
oschützki
, u. S
cholz
 & S. W
eise
: 
Metacrop 2.0. http://metacrop.ipk-gatersleben.de.
s
chubert
, i. & S. w
eise
. catalogue of chromosomal and Morpho-
logical Mutants of the broad bean, Vicia faba. http://www.
ipk-gatersleben.de/databases/vicia_faba_catalogue
W
eise
, S., u. S
cholz
, M.S. R
öder
 & i.e. M
atthies
: Metabrew: a com-
prehensive database of malting quality traits in brewing 
barley. http://metabrew.ipk-gatersleben.de.
w
illner
, e., S. W
eise
 & M. o
ppermann
: the european Poa database 
(ePdb). http://poa.ipk-gatersleben.de.
a
rend
,  d.,  l
ange
,  m.,  c
olmsee
,  c.,  f
lemming
,  s.,  c
hen
,  j.,  &  s
cholz
,  
u.: e!daL-Metadata-aPi – store cite and share primary data. 
http://edal.ipk-gatersleben.de.
c
hen
, d., M. c
hen
 & c. k
lukas
: Phenomics collaboration website. 
http://phenomics.cn.
c
olmsee
, c., k
eller
, e.r.j., o
ppermann
, m., s
enula
, a., z
anke
, c., f
unke
, 
t., w
eise
, s. & s
cholz
, u.: euRaLLiVeG Garlic and Shallot core 
collection (GScc). http://www.ipk-gatersleben.de/data-
bases/genetic_resources/gscc.
c
zauderna
, t. & F. S
chreiber
: SbGn-ed. http://www.sbgn-ed.org. 
d
ehmer
, k. & u. s
cholz
. Wild and cultivated potato species – GLkS 
passport and evaluation data. Genebank satellite collec-
tions Gross Luesewitz. http://pgrc.ipk-gatersleben.de/po-
tato/index.html
f
reytag
, u. & h. k
nüpffer
: Secondary evaluation of accessions of 
the genebank Gatersleben. http://pgrc.ipk-gatersleben.de/
eval/eval.html.
f
ritsch
, r.m.: Allium database. http://www.ipk-gatersleben.de/
en/gbisipk-gaterslebendegbis-i/special-collections/allium-
review/.
f
ritsch
, r.m. & s. w
eise
: taxonomic Allium Reference collection. 
http://www.ipk-gatersleben.de/databases/genetic_re-
sources/allium.
k
eller
, e.R.J. & M. o
ppermann
: the ecPGR european Allium data-
base. http://ealldb.ipk-gatersleben.de. 
k
eller
, e.R.J., c. z
anke
 & u. S
cholz
: euRaLLiVeG – Vegetative Al-
lium, europe’s core collection, Safe and Sound. http://eural-
liveg.ipk-gatersleben.de.
k
lukas
, c., d. c
hen
 & J.-M. P
ape
: iaP – the integrated analysis Plat-
form for high-througput Plant Phenotyping. http://iap.ipk-
gatersleben.de. 
k
nüpffer
,  h.,  s.  w
eise
  &  m.  o
ppermann
. ecPGR european barley 
database. http://www.ipk-gatersleben.de/databases/vi-
cia_faba_catalogue.
L
ange
, M., J. c
hen
 & u. S
cholz
: LaiLaPS – the Life Science Search 
engine. http://lailaps.ipk-gatersleben.de. 
M
atthies
, i.e., S. W
eise
, k. F
örster
 & M.S. R
öder
: association mapping 
and marker development of the candidate genes (1->3), 
(1->4)-β-d-Glucan-4-glucanohydrolase and (1->4)-β-Xylan-
endohydrolase 1 for malting quality in barley. http://pgrc.
ipk-gatersleben.de/glb , http://pgrc.ipk-gatersleben.de/X-1  
& http://pgrc.ipk-gatersleben.de/Phendat.
M
atthies
, i.e., S. W
eise
 & M.S. R
öder
: association of haplotype diver-
sity in the α-amylase gene amy1 with malting quality param-
eters in barley. http://pgrc.ipk-gatersleben.de/alpha-amylase. 
o
chsmann
, j., n. b
iermann
, r. n
arang
, m. o
ppermann
 & h. k
nüpffer
: 
Mansfeld’s World database of agricultural and horticultural 
crops (including Rehm’s database of useful tropical and 
Subtropical Plants). http://mansfeld.ipk-gatersleben.de/.
o
chsmann
, J. & R. n
arang
: taxcat2 – database of botanical taxo-
nomic categories http://mansfeld.ipk-gatersleben.de/tax-
cat2/.