TY - GEN
A1 - Wacker, Alexander
A1 - von Elert, Eric
T1 - Polyunsaturated fatty acids : evidence for non-substitutable biochemical resources in Daphnia galeata
N2 - The factors that determine the efficiency of energy transfer in aquatic food webs have been investigated for many decades. The plant-animal interface is the most variable and least predictable of all levels in the food web. In order to study determinants of food quality in a large lake and to test the recently proposed central importance of the long-chained eicosapentaenoic acid (EPA) at the pelagic producer-grazer interface, we tested the importance of polyunsaturated fatty acids (PUFAs) at the pelagic producerconsumer interface by correlating sestonic food parameters with somatic growth rates of a clone of Daphnia galeata. Daphnia growth rates were obtained from standardized laboratory experiments spanning one season with Daphnia feeding on natural seston from Lake Constance, a large pre-alpine lake. Somatic growth rates were fitted to sestonic parameters by using a saturation function. A moderate amount of variation was explained when the model included the elemental parameters carbon (r2 = 0.6) and nitrogen (r2 = 0.71). A tighter fit was obtained when sestonic phosphorus was incorporated (r2 = 0.86). The nonlinear regression with EPA was relatively weak (r2 = 0.77), whereas the highest degree of variance was explained by three C18-PUFAs. The best (r2 = 0.95), and only significant, correlation of Daphnia's growth was found with the C18-PUFA α-linolenic acid (α-LA; C18:3n-3). This correlation was weakest in late August when C:P values increased to 300, suggesting that mineral and PUFA-limitation of Daphnia's growth changed seasonally. Sestonic phosphorus and some PUFAs showed not only tight correlations with growth, but also with sestonic α-LA content. We computed Monte Carlo simulations to test whether the observed effects of α-LA on growth could be accounted for by EPA, phosphorus, or one of the two C18-PUFAs, stearidonic acid (C18:4n-3) and linoleic acid (C18:2n-6). With >99 % probability, the correlation of growth with α-LA could not be explained by any of these parameters. In order to test for EPA limitation of Daphnia's growth, in parallel with experiments on pure seston, growth was determined on seston supplemented with chemostat-grown, P-limited Stephanodiscus hantzschii, which is rich in EPA. Although supplementation increased the EPA content 80-800x, no significant changes in the nonlinear regression of the growth rates with α-LA were found, indicating that growth of Daphnia on pure seston was not EPA limited. This indicates that the two fatty acids, EPA and α-LA, were not mutually substitutable biochemical resources and points to different physiological functions of these two PUFAs. These results support the PUFA-limitation hypothesis for sestonic C:P < 300 but are contrary to the hypothesis of a general importance of EPA, since no evidence for EPA limitation was found. It is suggested that the resource ratios of EPA and α-LA rather than the absolute concentrations determine which of the two resources is limiting growth.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 063
KW - alga
KW - consumer
KW - Daphnia
KW - fatty acid
KW - food quality
KW - grazer
KW - herbivore
KW - Lake Constance
KW - European Alps
KW - PUFA
KW - seston
Y1 - 2001
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-17587
ER -
TY - GEN
A1 - Blenau, Wolfgang
A1 - Scheiner, Ricarda
A1 - Plückhahn, Stephanie
A1 - Oney, Bahar
A1 - Erber, Joachim
T1 - Behavioural pharmacology of octopamine, tyramine and dopamine in honey bees
N2 - In the honey bee, responsiveness to sucrose correlates with many behavioural parameters such as age of first foraging, foraging role and learning. Sucrose responsiveness can be measured using the proboscis extension response (PER) by applying sucrose solutions of increasing concentrations to the antenna of a bee. We tested whether the biogenic amines octopamine, tyramine and dopamine, and the dopamine receptor agonist 2-amino-6,7-dihydroxy-1,2,3,4-tetrahydronaphthalene (6,7-ADTN) can modulate sucrose responsiveness. The compounds were either injected into the thorax or fed in sucrose solution to compare different methods of application. Injection and feeding of tyramine or octopamine significantly increased sucrose responsiveness. Dopamine decreased sucrose responsiveness when injected into the thorax. Feeding of dopamine had no effect. Injection of 6,7-ADTN into the thorax and feeding of 6,7-ADTN reduced sucrose responsiveness significantly. These data demonstrate that sucrose responsiveness in honey bees can be modulated by biogenic amines, which has far reaching consequences for other types of behaviour in this insect. (C) 2002 Elsevier Science B.V. All rights reserved.
KW - Honey bee
KW - insect
KW - proboscis extension response
KW - sucrose responsiveness
KW - biogenic amines
Y1 - 2002
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44308
ER -
TY - GEN
A1 - Heinken, Thilo
A1 - Raudnitschka, Dorit
T1 - Do wild ungulates contribute to the dispersal of vascular plants in central European forests by epizoochory?
BT - A case study in NE Germany
BT - Eine Fallstudie aus Nordostdeutschland
N2 - The external dispersal ("epizoochory") of vascular plant diaspores (seeds and fruits) by roe deer and wild boar, i.e. the most common wild large mammals with a large home range in central Europe, was investigated in a 6.5-km² forest area in NE Germany dominated by mesic deciduous forests. The study involved brushing out the diaspores from the coats and hooves of 25 shot roe deer and nine wild boar. The results were compared with the forest vegetation of the study area. Whilst wild boar transported large amounts of various diaspores in the coat, the significance of roe deer for epizoochory was low due to their sleek fur and different behaviour compared to wild boar. Altogether, 55 vascular plant species were transported externally. Since only a limited number of seeds came from woodland habitats, the open landscape was at least as important as a source of attached seeds as the forest vegetation. Thus, most plant species occurring in the studied forest area, especially characteristic woodland herbs, showed no adaptations to epizoochorous dispersal, although being very abundant in the herb layer. We conclude that hoofed game play a particular role concerning the dispersal of ruderal and grassland species in the agricultural landscape of central Europe. However, the actual spread of some herb species in forests of northern Germany, e.g. Agrostis capillaris, Brachypodium sylvaticum, Deschampsia flexuosa, Galium aparine and Urtica dioica, may be mainly facilitated by wild ungulates. Though dispersal by large mammals is an important mechanism for long-distance dispersal of plants in general, our results suggest that most of the characteristic herb species of mesic deciduous forests have only low epizoochorous dispersal potentials. The implications for nature conservation and silviculture are discussed.
N2 - Die Ausbreitung von Gefäßpflanzen-Diasporen (Samen und Früchte) durch äußerliche Anhaftung ("Epizoochorie") an Rehen und Wildschweinen, den beiden häufigsten Schalenwild-Arten in Mitteleuropa, wurde im 6,5 km² großen Forst Brieselang bei Berlin (Bundesland Brandenburg) untersucht, in dem mesophile Laubwälder vorherrschen. Dazu wurden die Felle und Hufe von 25 geschossenen Rehen und neun Wildschweinen ausgekämmt und die Diasporen anschließend bestimmt. Die Ergebnisse wurden mit der Waldvegetation verglichen. Während Wildschweine große Mengen verschiedener Diasporentypen transportierten, war die Bedeutung von Rehen für die Ausbreitung von Pflanzen auf Grund des glatten Fells und der im Vergleich zum Wildschwein unterschiedlichen Verhaltensweisen wesentlich geringer. Insgesamt wurden 55 Phanerogamenarten epizoochor transportiert. Da nur ein kleiner Teil der ausgebreiteten Pflanzen Waldhabitate bevorzugt, war das Offenland eine mindestens ebenso wichtige Quelle anhaftender Diasporen wie die Waldvegetation. Die meisten Waldpflanzenarten wurden nicht ausgebreitet; insbesondere solche Arten, die ausschließlich in Wäldern wachsen, wurden nicht nachgewiesen. Viele Pflanzenarten sind – vermutlich auf Grund ihrer Diasporenmorphologie – weitgehend vom Transport ausgeschlossen, obwohl sie sehr häufig in der Krautschicht des untersuchten Waldes vorkommen. Daher ist Schalenwild in der Agrarlandschaft Mitteleuropas vermutlich vor allem für die Ausbreitung von Ruderal-, Segetal- und Grünlandpflanzen von Bedeutung. Die Ausbreitung einiger Pflanzenarten der Krautschicht in norddeutschen Wäldern z.B. Agrostis capillaris, Brachypodium sylvaticum, Deschampsia flexuosa, Galium aparine und Urtica dioica, könnte jedoch wesentlich auf Schalenwild zurückgehen. Obwohl Großsäuger insgesamt ein wichtiger Vektor für die Fernausbreitung von Pflanzen sind, zeigt unsere Studie, dass die meisten charakteristischen Waldbodenpflanzen mesophiler Laubwälder kaum ausgebreitet werden, also nur ein geringes epizoochores Ausbreitungspotenzial aufweisen. Die Bedeutung der Ergebnisse für den Waldnaturschutz und den Waldbau wird diskutiert.
T2 - Trägt Schalenwild durch Epizoochorie zur Ausbreitung von Gefäßpflanzen in mitteleuropäischen Wäldern bei?
KW - Diasporenmorphologie
KW - Epizoochorie
KW - Brandenburg
KW - Reh
KW - Waldbodenpflanzen
KW - Wildschwein
KW - diaspore morphology
KW - epizoochory
KW - forest plant species
KW - NE Germany
KW - roe deer
KW - wild boar
Y1 - 2002
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-5850
ER -
TY - GEN
A1 - Wacker, Alexander
A1 - von Elert, Eric
T1 - Strong influences of larval diet history on subsequent post-settlement growth in the freshwater mollusc Dreissena polymorpha
N2 - Significant seasonal variation in size at settlement has been observed in newly settled larvae of Dreissena polymorpha in Lake Constance. Diet quality, which varies temporally and spatially in freshwater habitats, has been suggested as a significant factor influencing life history and development of freshwater invertebrates. Accordingly, experiments were conducted with field-collected larvae to test the hypothesis that diet quality can determine planktonic larval growth rates, size at settlement and subsequent post-metamorphic growth rates. Larvae were fed one of two diets or starved. One diet was composed of cyanobacterial cells which are deficient in polyunsaturated fatty acids (PUFAs), and the other was a mixed diet rich in PUFAs. Freshly metamorphosed animals from the starvation treatment had a carbon content per individual 70% lower than that of larvae fed the mixed diet. This apparent exhaustion of larval internal reserves resulted in a 50% reduction of the postmetamorphic growth rates. Growth was also reduced in animals previously fed the cyanobacterial diet. Hence, low food quantity or low food quality during the larval stage of D. polymorpha lead to irreversible effects for postmetamorphic animals, and is related to inferior competitive abilities.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 064
KW - Dreissena polymorpha
KW - food quality
KW - fatty acid
KW - life history
KW - metamorphosis
KW - PUFA
Y1 - 2002
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-17627
ER -
TY - GEN
A1 - Blenau, Wolfgang
A1 - Grohmann, Lore
A1 - Erber, Joachim
A1 - Ebert, Paul R.
A1 - Strünker, Timo
A1 - Baumann, Arnd
T1 - Molecular and functional characterization of an octopamine receptor from honeybee (Apis mellifera) brain
N2 - Biogenic amines and their receptors regulate and modulate many physiological and behavioural processes in animals. In vertebrates, octopamine is only found in trace amounts and its function as a true neurotransmitter is unclear. In protostomes, however, octopamine can act as neurotransmitter, neuromodulator and neurohormone. In the honeybee, octopamine acts as a neuromodulator and is involved in learning and memory formation. The identification of potential octopamine receptors is decisive for an understanding of the cellular pathways involved in mediating the effects of octopamine. Here we report the cloning and functional characterization of the first octopamine receptor from the honeybee, Apis mellifera . The gene was isolated from a brain-specific cDNA library. It encodes a protein most closely related to octopamine receptors from Drosophila melanogaster and Lymnea stagnalis . Signalling properties of the cloned receptor were studied in transiently transfected human embryonic kidney (HEK) 293 cells. Nanomolar to micromolar concentrations of octopamine induced oscillatory increases in the intracellular Ca2+ concentration. In contrast to octopamine, tyramine only elicited Ca2+ responses at micromolar concentrations. The gene is abundantly expressed in many somata of the honeybee brain, suggesting that this octopamine receptor is involved in the processing of sensory inputs, antennal motor outputs and higher-order brain functions.
KW - Biogenic amine
KW - Ca2+
KW - cyclic AMP
KW - G protein-coupled receptor
KW - insect
Y1 - 2003
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44293
ER -
TY - GEN
A1 - Blenau, Wolfgang
A1 - Baumann, Arnd
T1 - Aminergic signal transduction in invertebrates : focus on tyramine and octopamine receptors
N2 - Electro-chemical signal transduction is the basis of communication between n eurons and their target cells. An important group of neuroactive substances that are released by action potentials from neurons are the biogenic amines. These a re small organic molecules that bind to specific receptors located in the target cell membrane. Once activated these receptors cause changes in the intracellula r concentration of second messengers, i.e. cyclic nucleotides, phosphoinositides , or Ca2+, leading to slow but long-lasting cellular responses. Biochemical, pha rmacological, physiological, and molecular biological approaches have unequivoca lly shown that biogenic amines are important regulators of cellular function in both vertebrates and invertebrates. In this review, we will concentrate on the p roperties of two biogenic amines and their receptors that were originally identi fied in invertebrates: tyramine and octopamine.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 107
Y1 - 2003
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44271
ER -
TY - GEN
A1 - Blenau, Wolfgang
A1 - Mustard, Julie A.
A1 - Hamilton, Ingrid S.
A1 - Ward, Vernon K.
A1 - Ebert, Paul R.
A1 - Mercer, Alison R.
T1 - Analysis of two D1-like dopamine receptors from the honey bee Apis mellifera reveals agonist-independent activity
N2 - Dopamine is found in many invertebrate organisms, including insects, however, the mechanisms through which this amine operates remain unclear. We have expressed two dopamine receptors cloned from honey bee (AmDOP1 and AmDOP2) in insect cells (Spodoptera frugiperda), and compared their pharmacology directly using production of cAMP as a functional assay. In each assay, AmDOP1 receptors required lower concentrations of dopamine and 6,7-ADTN for maximal activation than AmDOP2 receptors. Conversely, butaclamol and cis(Z)-flupentixol were more potent at blocking the cAMP response mediated through AmDOP2 than AmDOP1 receptors. Expression of AmDOP1, but not AmDOP2, receptors significantly increased levels of cAMP even in the absence of ligand. This constitutive activity was blocked by cis(Z)-flupentixol. This work provides the first evidence of a constitutively activated dopamine receptor in invertebrates and suggests that although AmDOP1 and AmDOP2 share much less homology than their vertebrate counterparts, they display a number of functional parallels with the mammalian D1-like dopamine receptors.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 109
KW - G protein-coupled receptor
KW - Biogenic amine
KW - Invertebrate
KW - cAMP
KW - Baculovirus
Y1 - 2003
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44378
ER -
TY - GEN
A1 - Hoppert, Michael
A1 - Reimer, Rudolph
A1 - Kemmling, Anne
A1 - Schröder, Annekatrin
A1 - Günzl, Bettina
A1 - Heinken, Thilo
T1 - Structure and reactivity of a biological soil crust from a xeric sandy soil in Central Europe
N2 - The investigation was designed to explore the structure, composition and activity of a biological soil crust on an acidic, sandy soil from a temperate climate. The crust covers several hundreds of square meters on the hilltop of a large terminal moraine. The conjugate alga Zygogonium ericetorum forms the essential matrix for the crust, a dense web of algal filaments with interspersed lichens and mosses. The crust is composed of three layers, with an uppermost layer consisting nearly entirely of a dense algal mat. In lower layers, a parasitic fungus, penetrating the algal cells, is another important component of the crust community. In this soil crust, photosynthetic and respiratory activity is stabilized at low water activities.
KW - biological soil crust
KW - desiccation tolerance
KW - electron microscopy
KW - Fusarium oxysporum
KW - Zygogonium ericetorum
Y1 - 2004
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-5872
ER -
TY - GEN
A1 - Köchy, Martin
A1 - Wilson, Scott D.
T1 - Variation in nitrogen deposition and available soil nitrogen in a forest–grassland ecotone in Canada
N2 - Regional variation in nitrogen (N) deposition increases plant productivity and decreases species diversity, but landscape- or local-scale influences on N deposition are less well-known. Using ion-exchange resin, we measured variation of N deposition and soil N availability within Elk Island National Park in the ecotone between grassland and boreal forest in western Canada. The park receives regionally high amounts of atmospheric N deposition (22 kg ha⁻¹ yr⁻¹). N deposition was on average higher ton clayrich luvisols than on brunisols, and areas burned 1 – 15 years previously received more atmospheric N than unburned sites. We suggest that the effects of previous fires and soil type on deposition rate act through differences in canopy structure. The magnitude of these effects varied with the presence of ungulate grazers (bison, moose, elk) and vegetation type (forest, shrubland, grassland). Available soil N (ammonium and nitrate) was higher in burned than unburned sites in the absence of grazing, suggesting an effect of deposition. On grazed sites, differences between fire treatments were small, presumably because the removal of biomass by grazers reduced the effect of fire. Aspen invades native grassland in this region, and our results suggest that fire without grazing might reinforce the expansion of forest into grassland facilitated by N deposition.
KW - fire
KW - grazing
KW - vegetation type
KW - soil type
KW - shrubland
KW - forest invasion
KW - subboreal
KW - aspen parkland
KW - Canada
Y1 - 2004
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-5768
ER -
TY - GEN
A1 - Heinken, Thilo
T1 - Migration of an annual myrmecochore
BT - a four year experiment with Melampyrum pratense L.
N2 - A seed sowing experiment was conducted in a mixed secondary woodland on acidic soils in NE Germany with Melampyrum pratense, an annual ant-dispersed forest herb which lacks a natural population in the study area, but is abundant in similar habitats. Each set of 300 seeds was sown within one square metre at three sites in 1997, and the development of the populations was recorded from 1998 onward. Additionally, seed fall patterns were studied in a natural population by means of adhesive cardboard. All trials resulted in the recruitment of populations, which survived and increased in both individual number and area, up to the year 2001. Thus, local distribution of Melampyrum pratense is dispersallimited. Total individual number increased from 105 to 3,390, and total population area from 2.07 to 109.04 m². Migration occurred in all directions. Mean migration rate was 0.91 m per year, and the highest migration rate was 6.48 m. No individual was recorded beyond 7.63 m from the centres of the sawn squares after three years, suggesting exclusive short-distance dispersal. As primary dispersal enables only distances of up to 0.25 m, ants are presumed to be the main dispersal vectors. Despite differences in individual number and colonization patterns, migration rates did not differ significantly between the populations, but were significantly higher in 2001 due to an increased population size. Colonization patterns were characterized by a rapid, negative exponential decrease of population density with increasing distance from the sown plot, suggesting a colonization by establishment of more or less isolated outposts of individuals and a subsequent gradual infill of the gaps between. My results resemble myrmecochorous dispersal distances in temperate woodlands, and migration rates and patterns across ecotones from ancient to recent deciduous forests. They may function as a colonization model of Melampyrum pratense after accidental long-distance dispersal.
KW - artificial introduction
KW - colonization
KW - dispersal
KW - myrmecochory
KW - NE Germany
KW - woodland herb
Y1 - 2004
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-5865
ER -
TY - GEN
A1 - Schultze, Rainer H.
A1 - Lemke, Matthias
A1 - Löhmannsröben, Hans-Gerd
T1 - Laser-induced fluorescence (LIF) spectroscopy for the in situ analysis of petroleum product-contaminated soils
N2 - Contents: Introduction Experimental Techniques: The LIF demonstrator unit - The LIF demonstrator unit - The mobile LIF spectrometer OPTIMOS - Investigated petroleum products and soil samples Results and Discussion: Photophysical properties of the petroleum products LIF spectroscopic investigations of oil-spiked samples LIF spectroscopic investigations of real-world soils Conclusions
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 9
Y1 - 2004
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-12271
ER -
TY - GEN
A1 - Heinken, Thilo
A1 - von Oheimb, Goddert
A1 - Schmidt, Marcus
A1 - Kriebitzsch, Wolf-Ulrich
A1 - Ellenberg, Hermann
T1 - Schalenwild breitet Gefäßpflanzen in der mitteleuropäischen Kulturlandschaft aus : ein erster Überblick
T1 - The dispersal by hoofed game of vascularplants in the Central European cultural landscape : a first overview
N2 - Im Norddeutschen Tiefland wurde die Ausbreitung von Gefäßpflanzen durch Rehe, Dam- und Rothirsche sowie Wildschweine untersucht. Diese Tiere transportieren zahlreiche Pflanzenarten in teilweise erheblichen Mengen über größere Distanzen, sowohl durch den Kot nach Darmpassage (Endozoochorie) als auch durch Anheftung an Fell und Schalen (Epizoochorie). Besondere Bedeutung kommt dabei Wildschweinen zu, die potenziell fast alle Pflanzenarten ausbreiten können. Bevorzugt werden im Wald wie im Offenland vorkommende Pflanzen und Arten des Offenlands ausgebreitet, während Arten mit enger Waldbindung nur in geringem Maße transportiert werden. Zoochorie durch Schalenwild bietet Erklärungsansätze sowohl für Ausbreitungsphänomene wie auch für das weitgehend fehlende Ausbreitungspotenzial vieler Pflanzenarten. Der Einfluss des Schalenwilds auf die Artenzusammensetzung und Gefäßpflanzen-Diversität in der mitteleuropäischen Kulturlandschaft sollte in seine naturschutzfachliche Neubewertung miteinbezogen werden. Die Einschränkung von Aktionsradien der Tiere durch die Zerschneidung von Lebensräumen sowie die Wildfütterung können für Ausbreitungsprozesse bisher kaum beachtete Konsequenzen haben.
N2 - The dispersal of vascular plants by roe deer, fallow deer, reed deer and wild boar was studied in the lowlands of northern Germany. Hoofed game species transport numerous plant species - partially in large amounts - over relatively long distances, both by faeces after gut passage (endozoochory) and by adhesion to coats and hooves (epizoochory). Wild boar are of particular importance as they potentially disperse almost all plant species. Species occurring both in forests and the open landscape as well as species of the open landscape are preferentially dispersed, while species restricted to forests are only transported to a minor degree. Patterns of zoochory by hoofed game provide explanations for dispersal phenomena and for the low dispersal potential of many plant species. Hoofed game's influence on species composition and phytodiversity in the Central European cultural landscape needs to be re-assessed in terms of its nature conservation relevance. The reduction of home ranges by habitat dissection and the feeding of game animals may have consequences for dispersal processes that have been underestimated until now.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 155
Y1 - 2005
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-46522
ER -
TY - GEN
A1 - Köchy, Martin
T1 - Opposite trends in life stages of annual plants caused by daily rainfall variability
BT - interaction with climate change
N2 - Global Circulation Models of climate predict not only a change of annual precipitation amounts but also a shift in the daily distribution. To improve the understanding of the importance of daily rain pattern for annual plant communities, which represent a large portion of semi-natural vegetation in the Middle East, I used a detailed, spatially explicit model. The model explicitly considers water storage in the soil and has been parameterized and validated with data collected in field experiments in Israel and data from the literature. I manipulated daily rainfall variability by increasing the mean daily rain intensity on rainy days (MDI, rain volume/day) and decreasing intervals between rainy days while keeping the mean annual amount constant. In factorial combination, I also increased mean annual precipitation (MAP). I considered five climatic regions characterized by 100, 300, 450, 600, and 800 mm MAP. Increasing MDI decreased establishment when MAP was >250 mm but increased establishment at more arid sites. The negative effect of increasing MDI was compensated by increasing mortality with increasing MDI in dry and typical Mediterranean regions (c. 360–720 mm MAP). These effects were strongly tied to water availability in upper and lower soil layers and modified by competition among seedlings and adults. Increasing MAP generally increased water availability, establishment, and density. The order of magnitudes of MDI and MAP effects overlapped partially so that their combined effect is important for projections of climate change effects on annual vegetation. The effect size of MAP and MDI followed a sigmoid curve along the MAP gradient indicating that the semi-arid region (≈300 mm MAP) is the most sensitive to precipitation change with regard to annual communitie
KW - Klimaänderung
KW - Klimawandel
KW - Einjahrespflanzen
KW - Schwankung
KW - tägliche Regenmenge
KW - Israel
KW - climate change
KW - daily rainfall variability
KW - annual plant
KW - Israel
Y1 - 2006
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-14699
SP - 347
EP - 357
ER -
TY - GEN
A1 - Scheiner, Ricarda
A1 - Baumann, Arnd
A1 - Blenau, Wolfgang
T1 - Aminergic control and modulation of honeybee behaviour
N2 - Biogenic amines are important messenger substances in the central nervous system and in peripheral organs of vertebrates and of invertebrates. The honeybee, Apis mellifera, is excellently suited to uncover the functions of biogenic amines in behaviour, because it has an extensive behavioural repertoire, with a number of biogenic amine receptors characterised in this insect. In the honeybee, the biogenic amines dopamine, octopamine, serotonin and tyramine modulate neuronal functions in various ways. Dopamine and serotonin are present in high concentrations in the bee brain, whereas octopamine and tyramine are less abundant. Octopamine is a key molecule for the control of honeybee behaviour. It generally has an arousing effect and leads to higher sensitivity for sensory inputs, better learning performance and increased foraging behaviour. Tyramine has been suggested to act antagonistically to octopamine, but only few experimental data are available for this amine. Dopamine and serotonin often have antagonistic or inhibitory effects as compared to octopamine. Biogenic amines bind to membrane receptors that primarily belong to the large gene-family of GTP-binding (G) protein coupled receptors. Receptor activation leads to transient changes in concentrations of intracellular second messengers such as cAMP, IP3 and/or Ca2+. Although several biogenic amine receptors from the honeybee have been cloned and characterised more recently, many genes still remain to be identified. The availability of the completely sequenced genome of Apis mellifera will contribute substantially to closing this gap. In this review, we will discuss the present knowledge on how biogenic amines and their receptor-mediated cellular responses modulate different behaviours of honeybees including learning processes and division of labour.
KW - Serotonin
KW - dopamine
KW - octopamine
KW - tyramine
KW - honeybee
Y1 - 2006
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-46106
ER -
TY - GEN
A1 - Köchy, Martin
A1 - Tielbörger, Katja
T1 - Hydrothermal time model of germination : parameters for 36 Mediterranean annual species based on a simplified approach
N2 - Germination rates and germination fractions of seeds can be predicted well by the hydrothermal time (HTT) model. Its four parameters hydrothermal time, minimum soil temperature, minimum soil moisture, and variation of minimum soil moisture, however, must be determined by lengthy germination experiments at combinations of several levels of soil temperature and moisture. For some applications of the HTT model it is more important to have approximate estimates for many species rather than exact values for only a few species. We suggest that minimum temperature and variation of minimum moisture can be estimated from literature data and expert knowledge. This allows to derive hydrothermal time and minimum moisture from existing data from germination experiments with one level of temperature and moisture. We applied our approach to a germination experiment comparing germination fractions of wild annual species along an aridity gradient in Israel. Using this simplified approach we estimated hydrothermal time and minimum moisture of 36 species. Comparison with exact data for three species shows that our method is a simple but effective method for obtaining parameters for the HTT model. Hydrothermal time and minimum moisture supposedly indicate climate related germination strategies. We tested whether these two parameters varied with the climate at the site where the seeds had been collected. We found no consistent variation with climate across species, suggesting that variation is more strongly controlled by site-specific factors.
N2 - Keimungsgeschwindigkeit und Anteil gekeimter Samen lassen sich gut mit dem Hydrothermalzeit-Modell bestimmen. Dessen vier Parameter Hydrothermalzeit, Mindesttemperatur, Mindestbodenfeuchte und Streuung der Mindestbodenfeuchte müssen jedoch durch aufwendige Keimungsversuche bei Kombinationen von mehreren Temperatur- und Feuchtigkeitsstufen bestimmt werden. Für manche Anwendungen des Hydrothermalzeit-Modells sind aber ungefähre Werte für viele Arten wichtiger als genaue Werte für wenige Arten. Wenn die Mindesttemperatur und die Streuung der Mindestfeuchte aus Veröffentlichungen und Expertenwissen geschätzt würde, können die Hydrothermalzeit und Mindestbodenfeuchte aus vorhandenen Daten von Keimungsversuchen mit nur einer Temperatur- und Feuchtigkeitsstufe berechnet werden. Wir haben unseren Ansatz auf einen Keimungsversuch zum Vergleich der Keimungsquote wilder einjähriger Arten entlang eines Trockenheitsgradienten in Israel angewendet. Mit diesem Ansatz bestimmten wir die Hydrothermalzeit und Mindestfeuchtigkeit von 36 Arten. Der Vergleich mit genauen Werten für drei Arten zeigt, dass mit unserem Ansatz Hydrothermalzeit-Parameter einfach und effektiv bestimmt werden können. Hydrothermalzeit und Mindestfeuchtigkeit sollten auch bestimmte klimabedingte Keimungsstrategien anzeigen. Deshalb testeten wir, ob diese zwei Parameter mit dem Klima am Ursprungsort der Samen zusammenhängen. Wir fanden jedoch keinen für alle Arten übereinstimmenden Zusammenhang, so dass die Unterschiede vermutlich stärker durch standörtliche als durch klimatische Ursachen hervorgerufen werden.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 022
KW - Keimungsrate
KW - Dormanz
KW - Hydrothermalzeit-Modell
KW - einjährige Pflanzen
KW - Mittelmeerraum
KW - germination rate
KW - dormancy
KW - hydrothermal time model
KW - annual plant species
KW - Mediterranean
Y1 - 2006
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-12406
ER -
TY - GEN
A1 - Köchy, Martin
T1 - Stochastic time series of daily precipitation for the interior of Israel
N2 - This contribution describes a generator of stochastic time series of daily precipitation for the interior of Israel from c. 90 to 900 mm mean annual precipitation (MAP) as a tool for studies of daily rain variability. The probability of rainfall on a given day of the year is described by a regular Gaussian peak curve function. The amount of rain is drawn randomly from an exponential distribution whose mean is the daily mean rain amount (averaged across years for each day of the year) described by a flattened Gaussian peak curve. Parameters for the curves have been calculated from monthly aggregated, long-term rain records from seven meteorological stations. Parameters for arbitrary points on the MAP gradient are calculated from a regression equation with MAP as the only independent variable. The simple structure of the generator allows it to produce time series with daily rain patterns that are projected under climate change scenarios and simultaneously control MAP. Increasing within-year variability of daily precipitation amounts also increases among-year variability of MAP as predicted by global circulation models. Thus, the time series incorporate important characteristics for climate change research and represent a flexible tool for simulations of daily vegetation or surface hydrology dynamics.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 029
KW - stochastische Zeitreihen
KW - täglicher Niederschlag
KW - Israel
KW - Klimawandel
KW - stochastic time series
KW - daily precipitation
KW - Israel
KW - climate change
Y1 - 2006
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-13155
ER -
TY - GEN
A1 - Blenau, Wolfgang
A1 - Hauser, Frank
A1 - Cazzamali, Giuseppe
A1 - Williamson, Michael
A1 - Grimmelikhuijzen, Cornelis J. P.
T1 - A review of neurohormone GPCRs present in the fruitfly Drosophila melanogaster and the honey bee Apis mellifera
N2 - G protein-coupled receptor (GPCR) genes are large gene families in every animal, sometimes making up to 1-2% of the animal's genome. Of all insect GPCRs, the neurohormone (neuropeptide, protein hormone, biogenic amine) GPCRs are especially important, because they, together with their ligands, occupy a high hierarchic position in the physiology of insects and steer crucial processes such as development, reproduction, and behavior. In this paper, we give a review of our current knowledge on Drosophila melanogaster GPCRs and use this information to annotate the neurohormone GPCR genes present in the recently sequenced genome from the honey bee Apis mellifera. We found 35 neuropeptide receptor genes in the honey bee (44 in Drosophila) and two genes, coding for leucine-rich repeats-containing protein hormone GPCRs (4 in Drosophila). In addition, the honey bee has 19 biogenic amine receptor genes (21 in Drosophila). The larger numbers of neurohormone receptors in Drosophila are probably due to gene duplications that occurred during recent evolution of the fly. Our analyses also yielded the likely ligands for 40 of the 56 honey bee neurohormone GPCRs identified in this study. In addition, we made some interesting observations on neurohormone GPCR evolution and the evolution and co-evolution of their ligands. For neuropeptide and protein hormone GPCRs, there appears to be a general co-evolution between receptors and their ligands. This is in contrast to biogenic amine GPCRs, where evolutionarily unrelated GPCRs often bind to the same biogenic amine, suggesting frequent ligand exchanges ("ligand hops") during GPCR evolution. (c) 2006 Elsevier Ltd. All rights reserved.
KW - GPCR
KW - neuropeptide
KW - neurohormone
KW - hormone
KW - biogenic amine
Y1 - 2006
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44326
ER -
TY - GEN
A1 - Heinken, Thilo
A1 - Schmidt, Marcus
A1 - von Oheimb, Goddert
A1 - Kriebitzsch, Wolf-Ulrich
A1 - Ellenberg, Hermann
T1 - Soil seed banks near rubbing trees indicate dispersal of plant species into forests by wild boar
N2 - Current knowledge about processes that generate long-distance dispersal of plants is still limited despite its importance for persistence of populations and colonization of new potential habitats. Today wild large mammals are presumed to be important vectors for long-distance transport of diaspores within and between European temperate forest patches, and in particular wild boars recently came into focus. Here we use a specific habit of wild boar, i.e. wallowing in mud and subsequent rubbing against trees, to evaluate epizoic dispersal of vascular plant diaspores. We present soil seed bank data from 27 rubbing trees versus 27 control trees from seven forest areas in Germany. The mean number of viable seeds and the plant species number were higher in soil samples near rubbing trees compared with control trees. Ten of the 20 most frequent species were more frequent, and many species exclusively appeared in the soil samples near rubbing trees. The large number of plant species and seeds – approximated > 1000 per tree – in the soils near rubbing trees is difficult to explain unless the majority were dispersed by wild boar. Hooked and bristly diaspores, i.e. those adapted to epizoochory, were more frequent, above that many species with unspecialised diaspores occurred exclusively near rubbing trees. Different to plant species closely tied to forest species which occur both in forest and open vegetation, and non-forest species were more frequent near rubbing trees compared with controls. These findings are consistent with previous studies on diaspore loads in the coats and hooves of shot wild boars. However, our method allows to identify the transport of diaspores from the open landscape into forest stands where they might especially emerge after disturbance, and a clustered distribution of epizoochorically dispersed seeds. Moreover, accumulation of seeds of wetness indicators near rubbing trees demonstrates directed dispersal of plant species inhabiting wet places between remote wallows.
N2 - Das aktuelle Wissen über Prozesse, die zur Fernausbreitung von Pflanzen führen, ist trotz ihrer Bedeutung für das Überleben von Populationen und die Besiedlung neuer potenzieller Habitate noch immer sehr begrenzt. Wildlebende Großsäuger sind heutzutage vermutlich wichtige Vektoren für den Ferntransport von Diasporen innerhalb und zwischen den einzelnen Waldflächen in Mitteleuropa, und speziell das Wildschwein (Sus scrofa L.) spielt dabei offenbar eine herausragende Rolle. Wir nutzen hier ein spezifisches Verhalten des Wildschweins – Suhlen im Schlamm und nachfolgendes Scheuern an sogenannten Malbäumen – um die epizoochore Ausbreitung von Gefäßpflanzen-Diasporen einzuschätzen. Dargestellt werden die Ergebnisse von Samenbank-Untersuchungen von 27 Malbäumen im Vergleich zu 27 Kontrollbäumen aus sieben Waldgebieten in Deutschland. Sowohl die mittlere Zahl lebensfähiger Samen als auch die Artenzahl waren höher in Bodenproben neben Malbäumen. Zehn der 20 in der Samenbank verbreitetsten Pflanzenarten hatten hier ihren Schwerpunkt, und viele Arten kamen ausschließlich in den neben Malbäumen gewonnenen Proben vor. Die große Zahl von Pflanzenarten und Samen – zumindest > 1000 pro Baum – im Boden an Malbäumen lässt sich nur durch die Aktivität der Wildschweine erklären. Mit Haken oder Borsten ausgestattete, d.h. an Epizoochorie angepasste Diasporen waren häufiger, aber auch viele Arten mit unspezialisierten Diasporen kamen ausschließlich in der Samenbank bei Malbäumen vor. Anders als weitgehend an Wald gebundene Pflanzenarten waren solche, die sowohl im Wald und im Offenland vorkommen, sowie nicht im Wald vorkommende Arten häufiger neben Malbäumen als neben Kontrollbäumen. Diese Befunde stimmen mit denen früherer Untersuchungen von Diasporenladungen im Fell und in den Hufen geschossener Wildschweine überein. Unsere Methode erlaubt darüber hinaus aber die Identifizierung des Diasporentransports aus dem Offenland in die Waldbestände, wo sie insbesondere nach Störungen keimen dürften, sowie einer ungleichmäßigen Verteilung epizoochor ausgebreiteter Diasporen. Außerdem zeigt die Akkumulation von Samen von Nässezeigern neben den Malbäumen eine gezielte Ausbreitung nasse Standorte bewohnender Pflanzenarten zwischen entfernt gelegenen Suhlen.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 150
KW - Diaspore morphology
KW - directed dispersal
KW - epizoochory
KW - long-distance dispersal
KW - Sus scrofa
Y1 - 2006
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-46476
ER -
TY - GEN
A1 - Schlenstedt, Jana
A1 - Balfanz, Sabine
A1 - Baumann, Arnd
A1 - Blenau, Wolfgang
T1 - Am5-HT7 : molecular and pharmacological characterization of the first serotonin receptor of the honeybee (Apis mellifera)
N2 - The biogenic amine serotonin (5-HT) plays a key role in the regulation and modulation of many physiological and behavioural processes in both vertebrates and invertebrates. These functions are mediated through the binding of serotonin to its receptors, of which 13 subtypes have been characterized in vertebrates. We have isolated a cDNA from the honeybee Apis mellifera (Am5-ht7) sharing high similarity to members of the 5-HT7 receptor family. Expression of the Am5-HT7 receptor in HEK293 cells results in an increase in basal cAMP levels, suggesting that Am5-HT7 is expressed as a constitutively active receptor. Serotonin application to Am5-ht7-transfected cells elevates cyclic adenosine 3',5'-monophosphate (cAMP) levels in a dose-dependent manner (EC50 = 1.1-1.8 nM). The Am5-HT7 receptor is also activated by 5-carboxamidotryptamine, whereas methiothepin acts as an inverse agonist. Receptor expression has been investigated by RT-PCR, in situ hybridization, and western blotting experiments. Receptor mRNA is expressed in the perikarya of various brain neuropils, including intrinsic mushroom body neurons, and in peripheral organs. This study marks the first comprehensive characterization of a serotonin receptor in the honeybee and should facilitate further analysis of the role(s) of the receptor in mediating the various central and peripheral effects of 5-HT.
KW - Behaviour
KW - biogenic amine
KW - cellular signalling
KW - constitutive activity
KW - cyclic AMP
Y1 - 2006
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44423
ER -
TY - GEN
A1 - Heinken, Thilo
T1 - Sand- und Silikat-Kiefernwälder (Dicrano-Pinion) in Deutschland : Gliederungskonzept und Ökologie
T1 - Pine forests on sandy and silicate soils (Dicrano-Pinion) in Germany : classification concept and ecology
N2 - In preparation for the „Synopsis of plant communities of Germany“ a comprehensive classification concept for the Scots pine forests on sandy and silicate soils is presented. On the basis of 2699 relevés from all natural provinces with important occurrences this classification for the first time integrates both northern and southern German forest stands. Pine forests are stable (“climax”) communities on three distinct habitat types at the drought and wetness limits of forest growth. In the phytosociological system these are reflected by the clearly separated syntaxa Erico-Pinetea (dry-calcareous), Dicrano-Pinion (dry-acidic) and Vaccinio uliginosi- Pinetea (wet-acidic). However, Pulsatillo-Pinetea (dry-moderate basicity) described in earlier publications cannot be separated floristically. In addition to the stable communities on extreme habitats pine forests of the mentioned syntaxa are widespread on potential mixed deciduous forest stands, especially after anthropogenic devastation and even beyond their original range. Six communites of the Dicrano-Pinion which also includes such secondary pine forest stands are occurring in Germany. They are presented in detail and classified according to their dynamic and edaphic differentiation. Lichen-rich pine forests (Cladonio- Pinetum) which grow on extremely dry and nutrient-poor sites are ecologically and floristically well-defined, though closely connected with other Dicrano-Pinion communities by forest succession. After separation of the Cladonio-Pinetum the Leucobryo-Pinetum is a speciespoor “central association” within the alliance. The Deschampsia flexuosa-Pinus-sylvestriscommunity is the most widespread forest type and dynamically and floristically passes into the mixed oak forests on acidic soils (Quercion roboris). On base-rich habitats the Empetro- Pinetum as endemic community of the southern Baltic Sea coasts, and the Peucedano-Pinetum in the northeastern and southern German inland are distinguished. The latter is found both on calcareous sands and primarily acidic sands which are secondary limed by calciferous pollutions. Finally, differences and similarities between the geographically separated northern and southern German Dicrano-Pinion forests are discussed in a biogeographic context, emphasising the advantages of the presented nation-wide classification concept.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 154
Y1 - 2007
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-46518
ER -
TY - GEN
A1 - Blenau, Wolfgang
A1 - Troppmann, Britta
A1 - Walz, Bernd
T1 - Pharmacology of serotonin-induced salivary secretion in Periplaneta americana
N2 - The acinar salivary gland of the cockroach, Periplaneta americana, is innervated by dopaminergic and serotonergic nerve fibers. Stimulation of the glands by serotonin (5-hydroxytryptamine, 5-HT) results in the production of a protein-rich saliva, whereas stimulation by dopamine results in saliva that is protein-free. Thus, dopamine acts selectively on ion-transporting peripheral cells within the acini, and 5-HT acts on protein-producing central cells. We have investigated the pharmacology of the 5-HT-induced secretory activity of isolated salivary glands of P. americana by testing several 5-HT receptor agonists and antagonists. The effects of 5-HT can be mimicked by the non-selective 5-HT receptor agonist 5-methoxytryptamine. All tested agonists that display at least some receptor subtype specificity in mammals, i.e., 5-carboxamidotryptamine, (+/-)-8-OH-DPAT, (+/-)-DOI, and AS 19, were ineffective in stimulating salivary secretion. 5-HT-induced secretion can be blocked by the vertebrate 5-HT receptor antagonists methiothepin, cyproheptadine, and mianserin. Our pharmacological data indicate that the pharmacology of arthropod 5-HT receptors is remarkably different from that of their vertebrate counterparts. (C) 2007 Elsevier Ltd. All rights reserved.
KW - Biogenic amine
KW - G protein-coupled receptor
KW - insect
KW - salivary gland
KW - secretion
Y1 - 2007
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44319
ER -
TY - GEN
A1 - Winkler, Eckart
A1 - Heinken, Thilo
T1 - Spread of an ant-dispersed annual herb : an individual-based simulation study on population development of Melampyrum pratense L.
N2 - The paper presents a simulation and parameter-estimation approach for evaluating stochastic patterns of population growth and spread of an annual forest herb, Melampyrum pratense (Orobanchaceae). The survival of a species during large-scale changes in land use and climate will depend, to a considerable extent, on its dispersal and colonisation abilities. Predictions on species migration need a combination of field studies and modelling efforts. Our study on the ability of M. pratense to disperse into so far unoccupied areas was based on experiments in secondary woodland in NE Germany. Experiments started in 1997 at three sites where the species was not yet present, with 300 seeds sown within one square meter. Population development was then recorded until 2001 by mapping of individuals with a resolution of 5 cm. Additional observations considered density dependence of seed production. We designed a spatially explicit individual-based computer simulation model to explain the spatial patterns of population development and to predict future population spread. Besides primary drop of seeds (barochory) it assumed secondary seed transport by ants (myrmecochory) with an exponentially decreasing dispersal tail. An important feature of populationpattern explanation was the simultaneous estimation of both population-growth and dispersal parameters from consistent spatio-temporal data sets. As the simulation model produced stochastic time series and random spatially discrete distributions of individuals we estimated parameters by minimising the expectation of weighted sums of squares. These sums-ofsquares criteria considered population sizes, radial population distributions around the area of origin and distributions of individuals within squares of 25*25 cm, the range of density action. Optimal parameter values, together with the precision of the estimates, were obtained from calculating sums of squares in regular grids of parameter values. Our modelling results showed that transport of fractions of seeds by ants over distances of 1…2 m was indispensable for explaining the observed population spread that led to distances of at most 8 m from population origin within 3 years. Projections of population development over 4 additional years gave a diffusion-like increase of population area without any “outposts”. This prediction generated by the simulation model gave a hypothesis which should be revised by additional field observations. Some structural deviations between observations and model output already indicated that for full understanding of population spread the set of dispersal mechanisms assumed in the model may have to be extended by additional features of plant-animal mutualism.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 152
KW - Pattern-oriented parameter estimation
KW - spatially explicit modelling
KW - individual-based model
KW - Melampyrum pratense
KW - seed dispersal
Y1 - 2007
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-46491
ER -
TY - GEN
A1 - Köchy, Martin
A1 - Bråkenhielm, Sven
T1 - Separation of effects of moderate N deposition from natural change in ground vegetation of forests and bogs
N2 - The effect of moderate rates of nitrogen deposition on ground floor vegetation is poorly predicted by uncontrolled surveys or fertilization experiments using high rates of nitrogen (N) addition. We compared the temporal trends of ground floor vegetation in permanent plots with moderate (7–13 kg ha−1 year−1) and lower bulk N deposition (4–6 kg ha−1 year−1) in southern Sweden during 1982–1998. We examined whether trends differed between growth forms (vascular plants and bryophytes) and vegetation types (three types of coniferous forest, deciduous forest, and bog). Trends of site-standardized cover and richness varied among growth forms, vegetation types, and deposition regions. Cover in spruce forests decreased at the same rate with both moderate and low deposition. In pine forests cover decreased faster with moderate deposition and in bogs cover decreased faster with low deposition. Cover of bryophytes in spruce forests increased at the same rate with both moderate and low deposition. In pine forests cover decreased faster with moderate deposition and in bogs and deciduous forests there was a strong non-linear increase with moderate deposition. The trend of number of vascular plants was constant with moderate and decreased with low deposition. We found no trend in the number of bryophyte species. We propose that the decrease of cover and number with low deposition was related to normal ecosystem development (increased shading), suggesting that N deposition maintained or increased the competitiveness of some species in the moderate-deposition region. Deposition had no consistent negative effect on vegetation suggesting that it is less important than normal successional processes.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 034
KW - Nitrogen deposition
KW - Vascular plants
KW - Bryophytes
KW - Species richness
KW - Succession
KW - Understorey
Y1 - 2008
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-16621
ER -
TY - GEN
A1 - Wulf, Monika
A1 - Heinken, Thilo
T1 - Colonization of recent coniferous versus deciduous forest stands by vascular plants at the local scale
N2 - Questions: 1. Are there differences among species in their preference for coniferous vs. deciduous forest? 2. Are tree and shrub species better colonizers of recent forest stands than herbaceous species? 3. Do colonization patterns of plant species groups depend on tree species composition? Location: Three deciduous and one coniferous recent forest areas in Brandenburg, NE Germany. Methods: In 34 and 21 transects in coniferous and deciduous stands, respectively, we studied the occurrence and percentage cover of vascular plants in a total of 150 plots in ancient stands, 315 in recent stands and 55 at the ecotone. Habitat preference, diaspore weight, generative dispersal potential and clonal extension were used to explain mechanisms of local migration. Regression analysis was conducted to test whether migration distance was related to species’ life-history traits. Results: 25 species were significantly associated with ancient stands and ten species were significantly more frequent in recent stands. Tree and shrub species were good colonizers of recent coniferous and deciduous stands. In the coniferous stands, all herbaceous species showed a strong dispersal limitation during colonization, whereas in the deciduous stands generalist species may have survived in the grasslands which were present prior to afforestation. Conclusions: The fast colonization of recent stands by trees and shrubs can be explained by their effective dispersal via wind and animals. This, and the comparably efficient migration of herbaceous forest specialists into recent coniferous stands, implies that the conversion of coniferous into deciduous stands adjacent to ancient deciduous forests is promising even without planting of trees.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 149
KW - Clonal growth
KW - diaspore weight
KW - dispersal potential
KW - forest specialist
KW - generalist emergent group
Y1 - 2008
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-46080
ER -
TY - GEN
A1 - Heinken, Thilo
T1 - Die natürlichen Kiefernstandorte Deutschlands und ihre Gefährdung
T1 - Natural Scots pine forests in Germany : habitats, distribution, and threat
N2 - Natürliche Standorte der Waldkiefer gibt es in Deutschland nur kleinflächig. Während Kiefernforste anstelle natürlicher Laubwälder heute oft landschaftsprägend sind, bildet die konkurrenzschwache und lichtbedürftige Kiefer ausschließlich auf extrem trockenen oder nassen, nährstoffarmen Standorten naturnahe Schlusswaldgesellschaften. Regionale Schwerpunkte liegen in subkontinentalen Regionen wie dem nordostdeutschen Tiefland und Bayern, ein „natürliches Kiefernareal" lässt sich aber kaum abgrenzen. An der Trockengrenze des Waldes finden sich auf Kalk- und Dolomitgesteinen artenreiche Karbonat-Trockenkiefernwälder mit Elementen der alpinen Rasen und Kalkmagerrasen in der Bodenvegetation. Diese Wälder besiedeln steile, südexponierte Felsen und morphodynamisch aktive Bereiche wie Rutschhänge und FlussSchotterböden im Umkreis der Alpen, kommen aber auch in den Mittelgebirgen vor. Ihr Gegenstück auf sauren Standorten sind die Sand- und Silikat-Kiefernwälder der Quarzsande und Sandstein-Verwitterungsböden, deren Bodenvegetation durch Zwergsträucher, Moose und Strauchflechten geprägt ist. Hier siedelt die Kiefer in den Tieflagen besonders auf Binnendünen und Sandern, aber auch auf Küstendünen der Ostsee, in den Mittelgebirgen z. B. auf den Sandsteinriffen der Sächsischen Schweiz. Der dritte Wuchsbereich natürlicher Kiefernwälder sind saure, nährstoffarme Moore, die ganz überwiegend von Regenwasser gespeist werden. Auch die Kiefern-Moorwälder sind in Nordostdeutschland und Bayern am häufigsten. Von diesen Standorten ausgehend, wo ihr Platz kaum von anderen Baumarten streitig gemacht wird, tritt die Waldkiefer immer wieder als Pionier auf weniger extremen Standorten auf. In der Naturlandschaft kam dies etwa nach Waldbränden oder Stürmen vor, doch der Mensch förderte die Kiefer durch Auflichtung der Wälder, Waldweide und Streunutzung stark. Auch die damit verbundene Nährstoffverarmung macht eine exakte Abgrenzung natürlicher Kiefernstandorte unmöglich. Die schlechtwüchsigen und forstwirtschaftlich nicht interessanten, ästhetisch aber sehr ansprechenden natürlichen Kiefernbestände sind heute vor allem durch Stickstoff-Immissionen gefährdet. Trotz ihrer oft kargen Erscheinung besitzen sie einen hohen Wert für die Biodiversität und den Artenschutz. Neben bodenbewohnenden Flechten und regionalen Relikt-Endemiten ist vor allem die in den letzten Jahrzehnten zunehmend gefährdete Vielfalt an Mykorrhiza-Pilzen hervorzuheben, die der Kiefer das Leben auf extrem nährstoffarmen Standorten überhaupt ermöglichen. Abschließend werden mögliche Schutz- bzw. Regenerationsmaßnahmen wie das Abplaggen flechtenreicher Kiefernstandorte vorgestellt.
N2 - Only small areas of natural Scots pine (Pinus sylvestris) habitat occur in Germany. Today pine plantations instead of natural deciduous forests often dominate the landscape. Yet, due to the competitive weakness and light demands of Scots pine, near-natural Scots pine climax communities are only found on extremely dry or wet, nutrient-poor sites, primarily in subcontinental regions of the north-eastern German lowlands and Bavaria. However, the "natural distribution range" of Scots pine is difficult to define. Species-rich, dry Scots pine forests, with alpine and calcareous grassland species in the ground vegetation, are found at the aridity limit of forests on sites with carbonate rich soils developed from limestone and dolomite parent material. These forests occur on steep south-facing slopes, on morphodynamically active areas such as landslides and coarse river gravel beds in and near the Alps, and also in the low mountain ranges. Scots pine forests are also found on acidic sites, on quartz sands and soils overlying weathered silicate rocks with an understorey dominated by dwarf shrubs, bryophytes and fruticose lichens. These forests are present in the lowlands, particularly on inland dunes and glacifluvial deposits, but also on coastal dunes around the Baltic Sea and in the low mountain ranges, for example on the sandstone cliffs in the Elbe Sandstone Mountains. Acidic, oligo-trophic bogs, mainly supplied by rainwater, comprise the third natural Scots pine forest habitat. These Scots pine bog forests occur most frequently in north-eastern Germany and in Bavaria. Coming from these habitats, where virtually no other tree species grows, Scots pine is found again and again as a pioneer on less extreme sites. In the natural landscape, it occurs mainly after forest fires and storms. Yet humans promote Scots pine by thinning forests, creating woodland pasture and removing litter. The nutrient depletion associated with these practices makes an exact delimitation of natural Scots pine habitats unfeasible. Natural pine forest stands, which, although attractive and appealing, grow poorly and are of little interest for forestry, are endangered mainly by anthropo-genic nitrogen depositions. Despite their meagre appearance, these forests are important for biodiversity and species conservation. In addition to terricolous lichens and regional relic endemic plant species, the diversity of mycorrhiza fungi, which enable Scots pine to exist on these nutrient-poor sites, increasingly is becoming endangered. Finally, possible conservation and regeneration practices, such as manually cutting sods in lichen-rich Scots pine forests, are presented.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 153
KW - Naturschutz
KW - Phytodiversität
KW - Pinus sylvestris
KW - Standort
KW - Walddynamik
KW - nature conservation
KW - phytodiversity
KW - Pinus sylvestris
KW - site conditions
KW - forest dynamics
Y1 - 2008
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-46506
ER -
TY - GEN
A1 - Rein, Julia
A1 - Voss, Martin
A1 - Blenau, Wolfgang
A1 - Walz, Bernd
A1 - Baumann, Otto
T1 - Hormone-induced assembly and activation of V-ATPase in blowfly salivary glands is mediated by protein kinase A
N2 - The vacuolar H+-ATPase (V-ATPase) in the apical membrane of blowfly (Calliphora vicina) salivary gland cells energizes the secretion of a KCl-rich saliva in response to the neurohormone serotonin (5-HT). We have shown previously that exposure to 5-HT induces a cAMP-mediated reversible assembly of V-0 and V-1 subcomplexes to V-ATPase holoenzymes and increases V-ATPase-driven proton transport. Here, we analyze whether the effect of cAMP on V-ATPase is mediated by protein kinase A (PKA) or exchange protein directly activated by cAMP (Epac), the cAMP target proteins that are present within the salivary glands. Immunofluorescence microscopy shows that PKA activators, but not Epac activators, induce the translocation of V1 components from the cytoplasm to the apical membrane, indicative of an assembly of V-ATPase holoenzymes. Measurements of transepithelial voltage changes and microfluorometric pH measurements at the luminal surface of cells in isolated glands demonstrate further that PKA-activating cAMP analogs increase cation transport to the gland lumen and induce a V-ATPase-dependent luminal acidification, whereas activators of Epac do not. Inhibitors of PKA block the 5-HT-induced V-1 translocation to the apical membrane and the increase in proton transport. We conclude that cAMP exerts its effects on V-ATPase via PKA.
KW - Vacuolar h+-atpase
KW - camp binding-sites
KW - cyclic-amp
KW - plasma-membrane
KW - drosophila-melanogaster
Y1 - 2008
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-46126
ER -
TY - GEN
A1 - Köchy, Martin
T1 - Effects of simulated daily precipitation patterns on annual plant populations depend on life stage and climatic region
N2 - Background: To improve the understanding of consequences of climate change for annual plant communities, I used a detailed, grid-based model that simulates the effect of daily rainfall variability on individual plants in five climatic regions on a gradient from 100 to 800 mm mean annual precipitation (MAP). The model explicitly considers moisture storage in the soil. I manipulated daily rainfall variability by changing the daily mean rain (DMR, rain volume on rainy days averaged across years for each day of the year) by ± 20%. At the same time I adjusted intervals appropriately between rainy days for keeping the mean annual volume constant. In factorial combination with changing DMR I also changed MAP by ± 20%. Results: Increasing MAP generally increased water availability, establishment, and peak shoot biomass. Increasing DMR increased the time that water was continuously available to plants in the upper 15 to 30 cm of the soil (longest wet period, LWP). The effect of DMR diminished with increasing humidity of the climate. An interaction between water availability and density-dependent germination increased the establishment of seedlings in the arid region, but in the more humid regions the establishment of seedlings decreased with increasing DMR. As plants matured, competition among individuals and their productivity increased, but the size of these effects decreased with the humidity of the regions. Therefore, peak shoot biomass generally increased with increasing DMR but the effect size diminished from the semiarid to the mesic Mediterranean region. Increasing DMR reduced via LWP the annual variability of biomass in the semiarid and dry Mediterranean regions. Conclusion: More rainstorms (greater DMR) increased the recharge of soil water reservoirs in more arid sites with consequences for germination, establishment, productivity, and population persistence. The order of magnitudes of DMR and MAP overlapped partially so that their combined effect is important for projections of climate change effects on annual vegetation.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 097
Y1 - 2008
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-33747
ER -
TY - GEN
A1 - Köchy, Martin
A1 - Mathaj, Martin
A1 - Jeltsch, Florian
A1 - Malkinson, Dan
T1 - Resilience of stocking capacity to changing climate in arid to Mediterranean landscapes
N2 - Small livestock is an important resource for rural human populations in dry climates. How strongly will climate change affect the capacity of the rangeland? We used hierarchical modelling to scale quantitatively the growth of shrubs and annual plants, the main food of sheep and goats, to the landscape extent in the eastern Mediterranean region. Without grazing, productivity increased in a sigmoid way with mean annual precipitation. Grazing reduced productivity more strongly the drier the landscape. At a point just under the stocking capacity of the vegetation, productivity declined precipitously with more intense grazing due to a lack of seed production of annuals. We repeated simulations with precipitation patterns projected by two contrasting IPCC scenarios. Compared to results based on historic patterns, productivity and stocking capacity did not differ in most cases. Thus, grazing intensity remains the stronger impact on landscape productivity in this dry region even in the future.
N2 - Kleinvieh ist eine wichtige Lebensgrundlage für die Landbevölkerung in trockenen Regionen. Wie stark wird sich der Klimawandel auf die Tragfähigkeit der Weideflächen auswirken? Wir benutzten hierarchische Modellierung, um das Wachstum von Sträuchern und einjährigen Kräutern, das wichtigste Futter für Ziegen und Schafe, quantitativ auf die Fläche von Landschaften in der östlichen Mittelmeerregion zu dimensionieren. Die Produktivität ohne Beweidung stieg sigmoidal mit dem mittleren Jahresniederschlag. Je trockener die Landschaft, desto stärker verminderte Beweidung die Produktion. An einem Punkt knapp unter der Tragfähigkeit der Vegetation, sank die Produktion stark mit zunehmender Beweidung, weil die Samenproduktion der Kräuter zu gering war. Wir wiederholten die Simulationen mit Niederschlagsverteilungsmustern gemäß zweier gegensätzlicher IPCC-Szenarien. Zukünftige Produktivität und Tragfähigkeit unterschieden sich in den meisten Fällen nicht von Ergebnissen auf Grund von historischer Niederschlagsverteilung. Allerdings war die zukünftige Produktivität in trockenen Habitaten der semiariden und trocken-mediterranen Regionen niedriger. Somit hat auch in Zukunft die Besatzdichte die größere Auswirkung auf die Produktivität dieser trockenen Landschaft als das Klima. "This abstract is provided by the authors, and is for convenience of the users only. The author certifies that the translation faithfully represents the official version in the language of the journal, which is the published Abstract of record and is the only Abstract to be used for reference and citation."
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 066
KW - topography
KW - spatially explicit model
KW - climate change
KW - Middle East
KW - stocking capacity
Y1 - 2008
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-18720
ER -
TY - GEN
A1 - Cox, Tom
A1 - Maris, Tom
A1 - Soetart, Karline
A1 - Conley, Daniel
A1 - van Damme, Stefan
A1 - Meire, Patrick
A1 - Middelburg, Jack J.
A1 - Vos, Matthijs
A1 - Struyf, Eric
T1 - A macro-tidal freshwater ecosystem recovering from hypereutrophication : the Schelde lease study
N2 - We report a 40 year record of eutrophication and hypoxia on an estuarine ecosystem and its recovery from hypereutrophication. After decades of high inorganic nutrient concentrations and recurring anoxia and hypoxia, we observe a paradoxical increase in chlorophyll-a concentrations with decreasing nutrient inputs. We hypothesise that algal growth was inhibited due to hypereutrophication, either by elevated ammonium concentrations, severe hypoxia or the production of harmful substances in such a reduced environment. We study the dynamics of a simple but realistic mathematical model, incorporating the assumption of algal growth inhibition. It shows a high algal biomass, net oxygen production equilibrium with low ammonia inputs, and a low algal biomass, net oxygen consumption equilibrium with high ammonia inputs. At intermediate ammonia inputs it displays two alternative stable states. Although not intentional, the numerical output of this model corresponds to observations, giving extra support for assumption of algal growth inhibition. Due to potential algal growth inhibition, the recovery of hypereutrophied systems towards a classical eutrophied state, will need reduction of waste loads below certain thresholds and will be accompanied by large fluctuations in oxygen concentrations. We conclude that also flow-through systems, heavily influenced by external forcings which partly mask internal system dynamics, can display multiple stable states.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 144
KW - Estuary SW Netherlands
KW - southern North-Sea
KW - Past 50 years
KW - Westerschelde estuary
KW - Marine ecosystems
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45180
ER -
TY - GEN
A1 - Childs, Liam H.
A1 - Nikoloski, Zoran
A1 - May, Patrick
A1 - Walther, Dirk
T1 - Identification and classification of ncRNA molecules using graph properties
N2 - The study of non-coding RNA genes has received increased attention in recent years fuelled by accumulating evidence that larger portions of genomes than previously acknowledged are transcribed into RNA molecules of mostly unknown function, as well as the discovery of novel non-coding RNA types and functional RNA elements. Here, we demonstrate that specific properties of graphs that represent the predicted RNA secondary structure reflect functional information. We introduce a computational algorithm and an associated web-based tool (GraPPLE) for classifying non-coding RNA molecules as functional and, furthermore, into Rfam families based on their graph properties. Unlike sequence-similarity-based methods and covariance models, GraPPLE is demonstrated to be more robust with regard to increasing sequence divergence, and when combined with existing methods, leads to a significant improvement of prediction accuracy. Furthermore, graph properties identified as most informative are shown to provide an understanding as to what particular structural features render RNA molecules functional. Thus, GraPPLE may offer a valuable computational filtering tool to identify potentially interesting RNA molecules among large candidate datasets.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 145
KW - RNA secondary structure
KW - Noncoding RNAs
KW - Structure prediction
KW - Gene-expression
KW - Structured RNAs
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45192
ER -
TY - GEN
A1 - Szymanski, Jedrzej
A1 - Jozefczuk, Szymon
A1 - Nikoloski, Zoran
A1 - Selbig, Joachim
A1 - Nikiforova, Victoria
A1 - Catchpole, Gareth
A1 - Willmitzer, Lothar
T1 - Stability of metabolic correlations under changing environmental conditions in Escherichia coli : a systems approach
N2 - Background: Biological systems adapt to changing environments by reorganizing their cellula r and physiological program with metabolites representing one important response level. Different stresses lead to both conserved and specific responses on the metabolite level which should be reflected in the underl ying metabolic network. Methodology/Principal Findings: Starting from experimental data obtained by a GC-MS based high-throughput metabolic profiling technology we here develop an approach that: (1) extracts network representations from metabolic conditiondependent data by using pairwise correlations, (2) determines the sets of stable and condition-dependent correlations based on a combination of statistical significance and homogeneity tests, and (3) can identify metabolites related to the stress response, which goes beyond simple ob servation s about the changes of metabolic concentrations. The approach was tested with Escherichia colias a model organism observed under four different environmental stress conditions (cold stress, heat stress, oxidative stress, lactose diau xie) and control unperturbed conditions. By constructing the stable network component, which displays a scale free topology and small-world characteristics, we demonstrated that: (1) metabolite hubs in this reconstructed correlation networks are significantly enriched for those contained in biochemical networks such as EcoCyc, (2) particular components of the stable network are enriched for functionally related biochemical path ways, and (3) ind ependently of the response scale, based on their importance in the reorganization of the cor relation network a set of metabolites can be identified which represent hypothetical candidates for adjusting to a stress-specific response. Conclusions/Significance: Network-based tools allowed the identification of stress-dependent and general metabolic correlation networks. This correlation-network-ba sed approach does not rely on major changes in concentration to identify metabolites important for st ress adaptation, but rather on the changes in network properties with respect to metabolites. This should represent a useful complementary technique in addition to more classical approaches.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 147
KW - Small-world networks
KW - saccharomyces-cerevisiae
KW - trehalose synthesis
KW - gene-expression
KW - stress-response
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45253
ER -
TY - GEN
A1 - Heinken, Thilo
A1 - Winkler, Eckart
T1 - Non-random dispersal by ants : long-term field data versus model predictions of population spread of a forest herb
N2 - Myrmecochory, i.e. dispersal of seeds by ants towards and around their nests, plays an important role in temperate forests. Yet hardly any study has examined plant population spread over several years and the underlying joint contribution of a hierarchy of dispersal modes and plant demography. We used a seed-sowing approach with three replicates to examine colonization patterns of Melampyrum pratense, an annual myrmecochorous herb, in a mixed Scots pine forest in northeastern Germany. Using a spatially explicit individualbased (SEIB) model population patterns over 4 years were explained by short-distance transport of seeds by small ant species with high nest densities, resulting in random spread. However, plant distributions in the field after another 4 years were clearly deviating from model predictions. Mean annual spread rate increased from 0.9 m to 5.1 m per year, with a clear inhomogeneous component. Obviously, after a lag-phase of several years, non-random seed dispersal by large red wood ants (Formica rufa) was determining the species’ spread, thus resulting in stratified dispersal due to interactions with different-sized ant species. Hypotheses on stratified dispersal, on dispersal lag, and on non-random dispersal were verified using an extended SEIB model, by comparison of model outputs with field patterns (individual numbers, population areas, and maximum distances). Dispersal towards red wood ant nests together with seed loss during transport and redistribution around nests were essential features of the model extension. The observed lag-phase in the initiation of non-random, medium-distance transport was probably due to a change of ant behaviour towards a new food source of increasing importance, being a meaningful example for a lag-phase in local plant species invasion. The results demonstrate that field studies should check model predictions wherever possible. Future research will show whether or not the M. pratense–ant system is representative for migration patterns of similar animal dispersal systems after having crossed range edges by long-distance dispersal events.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 151
KW - Melampyrum pratense
KW - population dynamics
KW - seed dispersal
KW - non-random dispersal
KW - plant-animal interaction
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-46482
ER -
TY - GEN
A1 - Schröder, Florian
A1 - Lisso, Janina
A1 - Lange, Peggy
A1 - Müssig, Carsten
T1 - The extracellular EXO protein mediates cell expansion in Arabidopsis leaves
N2 - Background: The EXO (EXORDIUM) gene was identified as a potential mediator of brassinosteroid (BR)-promoted growth. It is part of a gene family with eight members in Arabidopsis. EXO gene expression is under control of BR, and EXO overexpression promotes shoot and root growth. In this study, the consequences of loss of EXO function are described. Results: The exo loss of function mutant showed diminished leaf and root growth and reduced biomass production. Light and scanning electron microscopy analyses revealed that impaired leaf growth is due to reduced cell expansion. Epidermis, palisade, and spongy parenchyma cells were smaller in comparison to the wild-type. The exo mutant showed reduced brassinolide-induced cotyledon and hypocotyl growth. In contrast, exo roots were significantly more sensitive to the inhibitory effect of synthetic brassinolide. Apart from reduced growth, exo did not show severe morphological abnormalities. Gene expression analyses of leaf material identified genes that showed robust EXO-dependent expression. Growth-related genes such as WAK1, EXP5, and KCS1, and genes involved in primary and secondary metabolism showed weaker expression in exo than in wild-type plants. However, the vast majority of BR-regulated genes were normally expressed in exo. HA- and GFP-tagged EXO proteins were targeted to the apoplast. Conclusion: The EXO gene is essential for cell expansion in leaves. Gene expression patterns and growth assays suggest that EXO mediates BR-induced leaf growth. However, EXO does not control BR-levels or BR-sensitivity in the shoot. EXO presumably is involved in a signalling process which coordinates BR-responses with environmental or developmental signals. The hypersensitivity of exo roots to BR suggests that EXO plays a diverse role in the control of BR responses in the root.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 139
KW - Plant transformation
KW - Gene expression
KW - Wall proteins
KW - Thaliana
KW - Brassinosteroids
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45107
ER -
TY - GEN
A1 - Durek, Pawel
A1 - Schudoma, Christian
A1 - Weckwerth, Wolfram
A1 - Selbig, Joachim
A1 - Walther, Dirk
T1 - Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins
N2 - Background: Phosphorylation of proteins plays a crucial role in the regulation and activation of metabolic and signaling pathways and constitutes an important target for pharmaceutical intervention. Central to the phosphorylation process is the recognition of specific target sites by protein kinases followed by the covalent attachment of phosphate groups to the amino acids serine, threonine, or tyrosine. The experimental identification as well as computational prediction of phosphorylation sites (P-sites) has proved to be a challenging problem. Computational methods have focused primarily on extracting predictive features from the local, one-dimensional sequence information surrounding phosphorylation sites. Results: We characterized the spatial context of phosphorylation sites and assessed its usability for improved phosphorylation site predictions. We identified 750 non-redundant, experimentally verified sites with three-dimensional (3D) structural information available in the protein data bank (PDB) and grouped them according to their respective kinase family. We studied the spatial distribution of amino acids around phosphorserines, phosphothreonines, and phosphotyrosines to extract signature 3D-profiles. Characteristic spatial distributions of amino acid residue types around phosphorylation sites were indeed discernable, especially when kinase-family-specific target sites were analyzed. To test the added value of using spatial information for the computational prediction of phosphorylation sites, Support Vector Machines were applied using both sequence as well as structural information. When compared to sequence-only based prediction methods, a small but consistent performance improvement was obtained when the prediction was informed by 3D-context information. Conclusion: While local one-dimensional amino acid sequence information was observed to harbor most of the discriminatory power, spatial context information was identified as relevant for the recognition of kinases and their cognate target sites and can be used for an improved prediction of phosphorylation sites. A web-based service (Phos3D) implementing the developed structurebased P-site prediction method has been made available at http://phos3d.mpimp-golm.mpg.de.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 141
KW - Support vector machines
KW - Microarray data
KW - Docking interactions
KW - Signal-transduction
KW - Sequence alignment
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45129
ER -
TY - GEN
A1 - Mwinyi, Adina
A1 - Meyer, Achim
A1 - Bleidorn, Christoph
A1 - Lieb, Bernhard
A1 - Bartolomaeus, Thomas
A1 - Podsiadlowski, Lars
T1 - Mitochondrial genome sequence and gene order of Sipunculus nudus give additional support for an inclusion of Sipuncula into Annelida
N2 - Background: Mitochondrial genomes are a valuable source of data for analysing phylogenetic relationships. Besides sequence information, mitochondrial gene order may add phylogenetically useful information, too. Sipuncula are unsegmented marine worms, traditionally placed in their own phylum. Recent molecular and morphological findings suggest a close affinity to the segmented Annelida. Results: The first complete mitochondrial genome of a member of Sipuncula, Sipunculus nudus, is presented. All 37 genes characteristic for metazoan mtDNA were detected and are encoded on the same strand. The mitochondrial gene order (protein-coding and ribosomal RNA genes) resembles that of annelids, but shows several derivations so far found only in Sipuncula. Sequence based phylogenetic analysis of mitochondrial protein-coding genes results in significant bootstrap support for Annelida sensu lato, combining Annelida together with Sipuncula, Echiura, Pogonophora and Myzostomida. Conclusion: The mitochondrial sequence data support a close relationship of Annelida and Sipuncula. Also the most parsimonious explanation of changes in gene order favours a derivation from the annelid gene order. These results complement findings from recent phylogenetic analyses of nuclear encoded genes as well as a report of a segmental neural patterning in Sipuncula.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 124
KW - Transfer-rna genes; Phylogenetic analysis; Animal phylogeny; Control region; Sister Taxau
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44916
ER -
TY - GEN
A1 - May, Patrick
A1 - Christian, Jan-Ole
A1 - Kempa, Stefan
A1 - Walther, Dirk
T1 - ChlamyCyc : an integrative systems biology database and web-portal for Chlamydomonas reinhardtii
N2 - Background: The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern highthroughput technologies there is an imperative need to integrate large-scale data sets from highthroughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. Results: In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc) was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. Conclusion: ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 127
KW - Biochemical pathway database
KW - Gene-expression data
KW - Quantitative proteomics
KW - Metabolic pathways
KW - Genome annotation
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44947
ER -
TY - GEN
A1 - de Castro, Francisco
A1 - Gaedke, Ursula
A1 - Boenigk, Jens
T1 - Reverse evolution : driving forces behind the loss of acquired photosynthetic traits
N2 - Background: The loss of photosynthesis has occurred often in eukaryotic evolution, even more than its acquisition, which occurred at least nine times independently and which generated the evolution of the supergroups Archaeplastida, Rhizaria, Chromalveolata and Excavata. This secondary loss of autotrophic capability is essential to explain the evolution of eukaryotes and the high diversity of protists, which has been severely underestimated until recently. However, the ecological and evolutionary scenarios behind this evolutionary ‘‘step back’’ are still largely unknown. Methodology/Principal Findings: Using a dynamic model of heterotrophic and mixotrophic flagellates and two types of prey, large bacteria and ultramicrobacteria, we examine the influence of DOC concentration, mixotroph’s photosynthetic growth rate, and external limitations of photosynthesis on the coexistence of both types of flagellates. Our key premises are: large bacteria grow faster than small ones at high DOC concentrations, and vice versa; and heterotrophic flagellates are more efficient than the mixotrophs grazing small bacteria (both empirically supported). We show that differential efficiency in bacteria grazing, which strongly depends on cell size, is a key factor to explain the loss of photosynthesis in mixotrophs (which combine photosynthesis and bacterivory) leading to purely heterotrophic lineages. Further, we show in what conditions an heterotroph mutant can coexist, or even out-compete, its mixotrophic ancestor, suggesting that bacterivory and cell size reduction may have been major triggers for the diversification of eukaryotes. Conclusions/Significance: Our results suggest that, provided the mixotroph’s photosynthetic advantage is not too large, the (small) heterotroph will also dominate in nutrient-poor environments and will readily invade a community of mixotrophs and bacteria, due to its higher efficiency exploiting the ultramicrobacteria. As carbon-limited conditions were presumably widespread throughout Earth history, such a scenario may explain the numerous transitions from phototrophy to mixotrophy and further to heterotrophy within virtually all major algal lineages. We challenge prevailing concepts that affiliated the evolution of phagotrophy with eutrophic or strongly light-limited environments only.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 128
KW - Fresh-water habitats
KW - Operon copy number
KW - Growth-rate
KW - Bacteria
KW - Plankton
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44968
ER -
TY - GEN
A1 - Ebenhöh, Oliver
A1 - Handorf, Thomas
T1 - Functional classification of genome-scale metabolic networks
N2 - We propose two strategies to characterize organisms with respect to their metabolic capabilities. The first, investigative, strategy describes metabolic networks in terms of their capability to utilize different carbon sources, resulting in the concept of carbon utilization spectra. In the second, predictive, approach minimal nutrient combinations are predicted from the structure of the metabolic networks, resulting in a characteristic nutrient profile. Both strategies allow for a quantification of functional properties of metabolic networks, allowing to identify groups of organisms with similar functions. We investigate whether the functional description reflects the typical environments of the corresponding organisms by dividing all species into disjoint groups based on whether they are aerotolerant and/or photosynthetic. Despite differences in the underlying concepts, both measures display some common features. Closely related organisms often display a similar functional behavior and in both cases the functional measures appear to correlate with the considered classes of environments. Carbon utilization spectra and nutrient profiles are complementary approaches toward a functional classification of organism-wide metabolic networks. Both approaches contain different information and thus yield different clusterings, which are both different from the classical taxonomy of organisms. Our results indicate that a sophisticated combination of our approaches will allow for a quantitative description reflecting the lifestyles of organisms.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 129
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44975
ER -
TY - GEN
A1 - Kartal, Önder
A1 - Ebenhöh, Oliver
T1 - Ground state robustness as an evolutionary design principle in signaling networks
N2 - The ability of an organism to survive depends on its capability to adapt to external conditions. In addition to metabolic versatility and efficient replication, reliable signal transduction is essential. As signaling systems are under permanent evolutionary pressure one may assume that their structure reflects certain functional properties. However, despite promising theoretical studies in recent years, the selective forces which shape signaling network topologies in general remain unclear. Here, we propose prevention of autoactivation as one possible evolutionary design principle. A generic framework for continuous kinetic models is used to derive topological implications of demanding a dynamically stable ground state in signaling systems. To this end graph theoretical methods are applied. The index of the underlying digraph is shown to be a key topological property which determines the so-called kinetic ground state (or off-state) robustness. The kinetic robustness depends solely on the composition of the subdigraph with the strongly connected components, which comprise all positive feedbacks in the network. The component with the highest index in the feedback family is shown to dominate the kinetic robustness of the whole network, whereas relative size and girth of these motifs are emphasized as important determinants of the component index. Moreover, depending on topological features, the maintenance of robustness differs when networks are faced with structural perturbations. This structural off-state robustness, defined as the average kinetic robustness of a network’s neighborhood, turns out to be useful since some structural features are neutral towards kinetic robustness, but show up to be supporting against structural perturbations. Among these are a low connectivity, a high divergence and a low path sum. All results are tested against real signaling networks obtained from databases. The analysis suggests that ground state robustness may serve as a rationale for some structural peculiarities found in intracellular signaling networks.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 130
KW - Complex networks
KW - Transduction
KW - Motifs
KW - Cell
KW - Organization
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44982
ER -
TY - GEN
A1 - Zhang, Gong
A1 - Ignatova, Zoya
T1 - Generic algorithm to predict the speed of translational elongation : implications for protein biogenesis
N2 - Synonymous codon usage and variations in the level of isoaccepting tRNAs exert a powerful selective force on translation fidelity. We have developed an algorithm to evaluate the relative rate of translation which allows large-scale comparisons of the non-uniform translation rate on the protein biogenesis. Using the complete genomes of Escherichia coli and Bacillus subtilis we show that stretches of codons pairing to minor tRNAs form putative sites to locally attenuate translation; thereby the tendency is to cluster in near proximity whereas long contiguous stretches of slow-translating triplets are avoided. The presence of slow-translating segments positively correlates with the protein length irrespective of the protein abundance. The slow-translating clusters are predominantly located down-stream of the domain boundaries presumably to fine-tune translational accuracy with the folding fidelity of multidomain proteins. Translation attenuation patterns at highly structurally and functionally conserved domains are preserved across the species suggesting a concerted selective pressure on the codon selection and species-specific tRNA abundance in these regions.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 132
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45007
ER -
TY - GEN
A1 - Kugler, Annette
A1 - Köhler, Barbara
A1 - Palme, Klaus
A1 - Wolff, Patricia
A1 - Dietrich, Petra
T1 - Salt-dependent regulation of a CNG channel subfamily in Arabidopsis
N2 - Background: In Arabidopsis thaliana, the family of cyclic nucleotide-gated channels (CNGCs) is composed of 20 members. Previous studies indicate that plant CNGCs are involved in the control of growth processes and responses to abiotic and biotic stresses. According to their proposed function as cation entry pathways these channels contribute to cellular cation homeostasis, including calcium and sodium, as well as to stress-related signal transduction. Here, we studied the expression patterns and regulation of CNGC19 and CNGC20, which constitute one of the five CNGC subfamilies. Results: GUS, GFP and luciferase reporter assays were used to study the expression of CNGC19 and CNGC20 genes from Arabidopsis thaliana in response to developmental cues and salt stress. CNGC19 and CNGC20 were differentially expressed in roots and shoots. The CNGC19 gene was predominantly active in roots already at early growth stages. Major expression was observed in the phloem. CNGC20 showed highest promoter activity in mesophyll cells surrounding the veins. Its expression increased during development and was maximal in mature and senescent leaves. Both genes were upregulated in the shoot in response to elevated NaCl but not mannitol concentrations. While in the root, CNGC19 did not respond to changes in the salt concentration, in the shoot it was strongly upregulated in the observed time frame (6-72 hours). Salt-induction of CNGC20 was also observed in the shoot, starting already one hour after stress treatment. It occurred with similar kinetics, irrespective of whether NaCl was applied to roots of intact plants or to the petiole of detached leaves. No differences in K and Na contents of the shoots were measured in homozygous T-DNA insertion lines for CNGC19 and CNGC20, respectively, which developed a growth phenotype in the presence of up to 75 mM NaCl similar to that of the wild type. Conclusion: Together, the results strongly suggest that both channels are involved in the salinity response of different cell types in the shoot. Upon salinity both genes are upregulated within hours. CNGC19 and CNGC20 could assist the plant to cope with toxic effects caused by salt stress, probably by contributing to a re-allocation of sodium within the plant.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 133
KW - Nucleotide-gated channel
KW - Na+/H+ antiporter SOS1
KW - Ricinus-communis l
KW - Plasma membrane
KW - Functional analysis
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45019
ER -
TY - GEN
A1 - Schumann, Silvia
A1 - Terao, Mineko
A1 - Garattini, Enrico
A1 - Saggu, Miguel
A1 - Lendzian, Friedhelm
A1 - Hildebrandt, Peter
A1 - Leimkühler, Silke
T1 - Site directed mutagenesis of amino acid residues at the active site of mouse aldehyde oxidase AOX1
N2 - Mouse aldehyde oxidase (mAOX1) forms a homodimer and belongs to the xanthine oxidase family of molybdoenzymes which are characterized by an essential equatorial sulfur ligand coordinated to the molybdenum atom. In general, mammalian AOs are characterized by broad substrate specificity and an yet obscure physiological function. To define the physiological substrates and the enzymatic characteristics of mAOX1, we established a system for the heterologous expression of the enzyme in Eschericia coli. The recombinant protein showed spectral features and a range of substrate specificity similar to the native protein purified from mouse liver. The EPR data of recombinant mAOX1 were similar to those of AO from rabbit liver, but differed from the homologous xanthine oxidoreductase enzymes. Site-directed mutagenesis of amino acids Val806, Met884 and Glu1265 at the active site resulted in a drastic decrease in the oxidation of aldehydes with no increase in the oxidation of purine substrates. The double mutant V806E/M884R and the single mutant E1265Q were catalytically inactive enzymes regardless of the aldehyde or purine substrates tested. Our results show that only Glu1265 is essential for the catalytic activity by initiating the base-catalyzed mechanism of substrate oxidation. In addition, it is concluded that the substrate specificity of molybdo-flavoenzymes is more complex and not only defined by the three characterized amino acids in the active site.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 134
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45030
ER -
TY - GEN
A1 - Gärtner, Tanja
A1 - Steinfath, Matthias
A1 - Andorf, Sandra
A1 - Lisec, Jan
A1 - Meyer, Rhonda C.
A1 - Altmann, Thomas
A1 - Willmitzer, Lothar
A1 - Selbig, Joachim
T1 - Improved heterosis prediction by combining information on DNA- and metabolic markers
N2 - Background: Hybrids represent a cornerstone in the success story of breeding programs. The fundamental principle underlying this success is the phenomenon of hybrid vigour, or heterosis. It describes an advantage of the offspring as compared to the two parental lines with respect to parameters such as growth and resistance against abiotic or biotic stress. Dominance, overdominance or epistasis based models are commonly used explanations. Conclusion/Significance: The heterosis level is clearly a function of the combination of the parents used for offspring production. This results in a major challenge for plant breeders, as usually several thousand combinations of parents have to be tested for identifying the best combinations. Thus, any approach to reliably predict heterosis levels based on properties of the parental lines would be highly beneficial for plant breeding. Methodology/Principal Findings: Recently, genetic data have been used to predict heterosis. Here we show that a combination of parental genetic and metabolic markers, identified via feature selection and minimum-description-length based regression methods, significantly improves the prediction of biomass heterosis in resulting offspring. These findings will help furthering our understanding of the molecular basis of heterosis, revealing, for instance, the presence of nonlinear genotype-phenotype relationships. In addition, we describe a possible approach for accelerated selection in plant breeding.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 142
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45132
ER -
TY - GEN
A1 - Blenau, Wolfgang
A1 - Rotte, Cathleen
A1 - Krach, Christian
A1 - Balfanz, Sabine
A1 - Baumann, Arnd
A1 - Walz, Bernd
T1 - Molecular characterization and localization of the first tyramine receptor of the American cockroach (Periplaneta americana)
N2 - The phenolamines octopamine and tyramine control, regulate, and modulate many physiological and behavioral processes in invertebrates. Vertebrates possess only small amounts of both substances, and thus, octopamine and tyramine, together with other biogenic amines, are referred to as “trace amines.” Biogenic amines evoke cellular responses by activating G-protein-coupled receptors. We have isolated a complementary DNA (cDNA) that encodes a biogenic amine receptor from the American cockroach Periplaneta americana, viz., Peatyr1, which shares high sequence similarity to members of the invertebrate tyramine-receptor family. The PeaTYR1 receptor was stably expressed in human embryonic kidney (HEK) 293 cells, and its ligand response has been examined. Receptor activation with tyramine reduces adenylyl cyclase activity in a dose-dependent manner (EC50 350 nM). The inhibitory effect of tyramine is abolished by co-incubation with either yohimbine or chlorpromazine. Receptor expression has been investigated by reverse transcription polymerase chain reaction and immunocytochemistry. The mRNA is present in various tissues including brain, salivary glands, midgut, Malpighian tubules, and leg muscles. The effect of tyramine on salivary gland acinar cells has been investigated by intracellular recordings, which have revealed excitatory presynaptic actions of tyramine. This study marks the first comprehensive molecular, pharmacological, and functional characterization of a tyramine receptor in the cockroach.
KW - Biogenic amine
KW - cellular signaling
KW - G-protein-coupled receptor
KW - octopamine
KW - salivary gland
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44335
ER -
TY - GEN
A1 - Voss, Martin
A1 - Blenau, Wolfgang
A1 - Walz, Bernd
A1 - Baumann, Otto
T1 - V-ATPase deactivation in blowfly salivary glands is mediated by protein phosphatase 2C
N2 - The activity of vacuolar H+-ATPase (V-ATPase) in the apical membrane of blowfly (Calliphora vicina) salivary glands is regulated by the neurohormone serotonin (5-HT). 5-HT induces, via protein kinase A, the phosphorylation of V-ATPase subunit C and the assembly of V-ATPase holoenzymes. The protein phosphatase responsible for the dephosphorylation of subunit C and V-ATPase inactivation is not as yet known. We show here that inhibitors of protein phosphatases PP1 and PP2A (tautomycin, ocadaic acid) and PP2B (cyclosporin A, FK-506) do not prevent V-ATPase deactivation and dephosphorylation of subunit C. A decrease in the intracellular Mg2+ level caused by loading secretory cells with EDTA-AM leads to the activation of proton pumping in the absence of 5-HT, prolongs the 5-HT-induced response in proton pumping, and inhibits the dephosphorylation of subunit C. Thus, the deactivation of V-ATPase is most probably mediated by a protein phosphatase that is insensitive to okadaic acid and that requires Mg2+, namely, a member of the PP2C protein family. By molecular biological techniques, we demonstrate the expression of at least two PP2C protein family members in blowfly salivary glands. © 2009 Wiley Periodicals, Inc.
KW - vacuolar H+-ATPase
KW - assembly
KW - regulation
KW - protein phosphatise
KW - dephosphorylation
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44360
ER -
TY - GEN
A1 - Steinfath, Matthias
A1 - Gärtner, Tanja
A1 - Lisec, Jan
A1 - Meyer, Rhonda C.
A1 - Altmann, Thomas
A1 - Willmitzer, Lothar
A1 - Selbig, Joachim
T1 - Prediction of hybrid biomass in Arabidopsis thaliana by selected parental SNP and metabolic markers
T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2 - A recombinant inbred line (RIL) population, derived from two Arabidopsis thaliana accessions, and the corresponding testcrosses with these two original accessions were used for the development and validation of machine learning models to predict the biomass of hybrids. Genetic and metabolic information of the RILs served as predictors. Feature selection reduced the number of variables (genetic and metabolic markers) in the models by more than 80% without impairing the predictive power. Thus, potential biomarkers have been revealed. Metabolites were shown to bear information on inherited macroscopic phenotypes. This proof of concept could be interesting for breeders. The example population exhibits substantial mid-parent biomass heterosis. The results of feature selection could therefore be used to shed light on the origin of heterosis. In this respect, mainly dominance effects were detected.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1324
KW - Quantitative Trait Locus
KW - feature selection
KW - Partial Little Square
KW - recombinant inbred line
KW - Quantitative Trait Locus analysis
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431115
SN - 1866-8372
IS - 1324
ER -
TY - GEN
A1 - Meyer, Rhonda Christiane
A1 - Kusterer, Barbara
A1 - Lisec, Jan
A1 - Steinfath, Matthias
A1 - Becher, Martina
A1 - Scharr, Hanno
A1 - Melchinger, Albrecht E.
A1 - Selbig, Joachim
A1 - Schurr, Ulrich
A1 - Willmitzer, Lothar
A1 - Altmann, Thomas
T1 - QTL analysis of early stage heterosis for biomass in Arabidopsis
T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2 - The main objective of this study was to identify genomic regions involved in biomass heterosis using QTL, generation means, and mode-of-inheritance classification analyses. In a modified North Carolina Design III we backcrossed 429 recombinant inbred line and 140 introgression line populations to the two parental accessions, C24 and Col-0, whose F 1 hybrid exhibited 44% heterosis for biomass. Mid-parent heterosis in the RILs ranged from −31 to 99% for dry weight and from −58 to 143% for leaf area. We detected ten genomic positions involved in biomass heterosis at an early developmental stage, individually explaining between 2.4 and 15.7% of the phenotypic variation. While overdominant gene action was prevalent in heterotic QTL, our results suggest that a combination of dominance, overdominance and epistasis is involved in biomass heterosis in this Arabidopsis cross.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1330
KW - Quantitative Trait Locus
KW - recombinant inbred line
KW - Quantitative Trait Locus analysis
KW - dominance effect
KW - recombinant inbred line population
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431272
SN - 1866-8372
IS - 1330
ER -
TY - GEN
A1 - Bleidorn, Christoph
A1 - Podsiadlowski, Lars
A1 - Zhong, Min
A1 - Eeckhaut, Igor
A1 - Hartmann, Stefanie
A1 - Halanych, Kenneth M.
A1 - Tiedemann, Ralph
T1 - On the phylogenetic position of Myzostomida : can 77 genes get it wrong?
N2 - Background: Phylogenomic analyses recently became popular to address questions about deep metazoan phylogeny. Ribosomal proteins (RP) dominate many of these analyses or are, in some cases, the only genes included. Despite initial hopes, hylogenomic analyses including tens to hundreds of genes still fail to robustly place many bilaterian taxa. Results: Using the phylogenetic position of myzostomids as an example, we show that phylogenies derived from RP genes and mitochondrial genes produce incongruent results. Whereas the former support a position within a clade of platyzoan taxa, mitochondrial data recovers an annelid affinity, which is strongly supported by the gene order data and is congruent with morphology. Using hypothesis testing, our RP data significantly rejects the annelids affinity, whereas a platyzoan relationship is significantly rejected by the mitochondrial data. Conclusion: We conclude (i) that reliance of a set of markers belonging to a single class of macromolecular complexes might bias the analysis, and (ii) that concatenation of all available data might introduce conflicting signal into phylogenetic analyses. We therefore strongly recommend testing for data incongruence in phylogenomic analyses. Furthermore, judging all available data, we consider the annelid affinity hypothesis more plausible than a possible platyzoan affinity for myzostomids, and suspect long branch attraction is influencing the RP data. However, this hypothesis needs further confirmation by future analyses.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 123
KW - Cirriferum myzostomida
KW - Mitochondrial genomes
KW - Transfer-rna
KW - Data sets
KW - Sequence
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44893
ER -
TY - GEN
A1 - Ziege, Madlen
A1 - Mahlow, Kristin
A1 - Hennige-Sulz, Carmen
A1 - Kronmarck, Claudia
A1 - Tiedemann, Ralph
A1 - Streit, Bruno
A1 - Plath, Martin
T1 - Audience effects in the Atlantic molly (Poecilia mexicana) : prudent male mate choice in response to perceived sperm competition risk?
N2 - Background: Multidirectional interactions in social networks can have a profound effect on mate choice behavior; e.g., Poecilia mexicana males show weaker expression of mating preferences when being observed by a rival. This may be an adaptation to reduce sperm competition risk, which arises because commonly preferred female phenotypes will receive attention also from surrounding males, and/or because other males can copy the focal male's mate choice. Do P. mexicana males indeed respond to perceived sperm competition risk? We gave males a choice between two females and repeated the tests under one of the following conditions: (1) an empty transparent cylinder was presented (control); (2) another ("audience") male inside the cylinder observed the focal male throughout the 2nd part, or (3) the audience male was presented only before the tests, but could not eavesdrop during the actual choice tests (non-specific sperm competition risk treatments); (4) the focal male could see a rival male interact sexually with the previously preferred, or (5) with the non-preferred female before the 2nd part of the tests (specific sperm competition risk treatments). Results: The strength of individual male preferences declined slightly also during the control treatment (1). However, this decrease was more than two-fold stronger in audience treatment (2), i.e., with non-specific sperm competition risk including the possibility for visual eavesdropping by the audience male. No audience effect was found in treatments (3) and (5), but a weak effect was also observed when the focal male had seen the previously preferred female sexually interact with a rival male (treatment 4; specific sperm competition risk). Conclusion: When comparing the two 'non-specific sperm competition risk' treatments, a very strong effect was found only when the audience male could actually observe the focal male during mate choice [treatment (2)]. This suggests that focal males indeed attempt to conceal their mating preferences so as to prevent surrounding males from copying their mate choice. When there is no potential for eavesdropping [treatment (3)], non-specific specific sperm competition risk seems to play a minor or no role. Our results also show that P. mexicana males tend to share their mating effort more equally among females when the resource value of their previously preferred mate decreases after mating with a rival male (perceived specific sperm competition risk), but this effect is comparatively weak.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 143
KW - Siamese fighting fish
KW - Guppies poecilia-reticulata
KW - Betta-splendens
KW - Public information
KW - Mating preferences
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45171
ER -
TY - GEN
A1 - Blenau, Wolfgang
A1 - Rotte, Cathleen
A1 - Witte, Jeannine
A1 - Baumann, Otto
A1 - Walz, Bernd
T1 - Source, topography and excitatory effects of GABAergic innervation in cockroach salivary glands
N2 - Cockroach salivary glands are innervated by dopaminergic and serotonergic neurons. Both transmitters elicit saliva secretion. We studied the distribution pattern of neurons containing gamma-aminobutyric acid ( GABA) and their physiological role. Immunofluorescence revealed a GABA-immunoreactive axon that originates within the subesophageal ganglion at the salivary neuron 2 (SN2) and this extends within the salivary duct nerve towards the salivary gland. GABA-positive fibers form a network on most acinar lobules and a dense plexus in the interior of a minor fraction of acinar lobules. Co-staining with anti-synapsin revealed that some putative GABAergic terminals seem to make pre-synaptic contacts with GABA-negative release sites. Many putative GABAergic release sites are at some distance from other synapses and at distance from the acinar tissue. Intracellular recordings from isolated salivary glands have revealed that GABA does not affect the basolateral membrane potential of the acinar cells directly. When applied during salivary duct nerve stimulation, GABA enhances the electrical response of the acinar cells and increases the rates of fluid and protein secretion. The effect on electrical cell responses is mimicked by the GABA(B) receptor agonists baclofen and SKF97541, and blocked by the GABAB receptor antagonists CGP52432 and CGP54626. These findings indicate that GABA has a modulatory role in the control of salivation, acting presynaptically on serotonergic and/or dopaminergic neurotransmission.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 111
KW - GABA
KW - salivary gland
KW - innervation
KW - cockroach
KW - Periplaneta americana
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44353
ER -
TY - GEN
A1 - Szarzynska, Bogna
A1 - Sobkowiak, Lukasz
A1 - Pant, Bikram Datt
A1 - Balazadeh, Salma
A1 - Scheible, Wolf-Rüdiger
A1 - Müller-Röber, Bernd
A1 - Jarmolowski, Artur
A1 - Szweykowska-Kulinska, Zofia
T1 - Gene structures and processing of Arabidopsis thaliana HYL1-dependent pri-miRNAs
N2 - Arabidopsis thaliana HYL1 is a nuclear doublestranded RNA-binding protein involved in the maturation of pri-miRNAs. A quantitative real-time PCR platform for parallel quantification of 176 primiRNAs was used to reveal strong accumulation of 57 miRNA precursors in the hyl1 mutant that completely lacks HYL1 protein. This approach enabled us for the first time to pinpoint particular members of MIRNA family genes that require HYL1 activity for efficient maturation of their precursors. Moreover, the accumulation of miRNA precursors in the hyl1 mutant gave us the opportunity to carry out 3’ and 5’ RACE experiments which revealed that some of these precursors are of unexpected length. The alignment of HYL1- dependent miRNA precursors to A. thaliana genomic sequences indicated the presence of introns in 12 out of 20 genes studied. Some of the characterized intron-containing pri-miRNAs undergo alternative splicing such as exon skipping or usage of alternative 5’ splice sites suggesting that this process plays a role in the regulation of miRNA biogenesis. In the hyl1 mutant intron-containing pri-miRNAs accumulate alongside spliced primiRNAs suggesting the recruitment of HYL1 into the miRNA precursor maturation pathway before their splicing occurs.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 138
KW - Binding-protein hyl1
KW - Abscisic-acid
KW - Flowering time
KW - Micro-RNA
KW - Serrate
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45085
ER -
TY - GEN
A1 - Riano-Pachon, Diego Mauricio
A1 - Nagel, Axel
A1 - Neigenfind, Jost
A1 - Wagner, Robert
A1 - Basekow, Rico
A1 - Weber, Elke
A1 - Müller-Röber, Bernd
A1 - Diehl, Svenja
A1 - Kersten, Birgit
T1 - GabiPD : the GABI primary database - a plant integrative "omics" database
N2 - The GABI Primary Database, GabiPD (http:// www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different ‘omics’ fronts are incorporated (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for textbased retrieval of all data types in GabiPD (e.g. clones, genes, mutant lines). All data types point to a central Gene GreenCard, where gene information is integrated from genome projects or NCBI UniGene sets. The centralized Gene GreenCard allows visualizing ESTs aligned to annotated transcripts as well as displaying identified protein domains and gene structure. Moreover, GabiPD makes available interactive genetic maps from potato and barley, and protein 2DE gels from Arabidopsis thaliana and Brassica napus. Gene expression and metabolic-profiling data can be visualized through MapManWeb. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of the data.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 137
KW - Phosphorylation sites
KW - Arabidopsis thaliana
KW - Information
KW - Proteins
KW - Families
Y1 - 2009
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45075
ER -
TY - GEN
A1 - Plath, Martin
A1 - Hermann, Bernd
A1 - Schröder, Christine
A1 - Riesch, Rüdiger
A1 - Tobler, Michael
A1 - García de León, Francisco J.
A1 - Schlupp, Ingo
A1 - Tiedemann, Ralph
T1 - Locally adapted fish populations maintain small-scale genetic differentiation despite perturbation by a catastrophic flood event
N2 - Background: Local adaptation to divergent environmental conditions can promote population genetic differentiation even in the absence of geographic barriers and hence, lead to speciation. Perturbations by catastrophic events, however, can distort such parapatric ecological speciation processes. Here, we asked whether an exceptionally strong flood led to homogenization of gene pools among locally adapted populations of the Atlantic molly (Poecilia mexicana, Poeciliidae) in the Cueva del Azufre system in southern Mexico, where two strong environmental selection factors (darkness within caves and/or presence of toxic H2S in sulfidic springs) drive the diversification of P. mexicana. Nine nuclear microsatellites as well as heritable female life history traits (both as a proxy for quantitative genetics and for trait divergence) were used as markers to compare genetic differentiation, genetic diversity, and especially population mixing (immigration and emigration) before and after the flood. Results: Habitat type (i.e., non-sulfidic surface, sulfidic surface, or sulfidic cave), but not geographic distance was the major predictor of genetic differentiation. Before and after the flood, each habitat type harbored a genetically distinct population. Only a weak signal of individual dislocation among ecologically divergent habitat types was uncovered (with the exception of slightly increased dislocation from the Cueva del Azufre into the sulfidic creek, El Azufre). By contrast, several lines of evidence are indicative of increased flood-induced dislocation within the same habitat type, e.g., between different cave chambers of the Cueva del Azufre. Conclusions: The virtual absence of individual dislocation among ecologically different habitat types indicates strong natural selection against migrants. Thus, our current study exemplifies that ecological speciation in this and other systems, in which extreme environmental factors drive speciation, may be little affected by temporary perturbations, as adaptations to physico-chemical stressors may directly affect the survival probability in divergent habitat types.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 162
Y1 - 2010
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-48599
ER -
TY - GEN
A1 - Troppmann, Britta
A1 - Balfanz, Sabine
A1 - Baumann, Arnd
A1 - Blenau, Wolfgang
T1 - Inverse agonist and neutral antagonist actions of synthetic compounds at an insect 5-HT1 receptor
N2 - Background and purpose: 5-Hydroxytryptamine (5-HT) has been shown to control and modulate many physiological and behavioural functions in insects. In this study, we report the cloning and pharmacological properties of a 5-HT1 receptor of an insect model for neurobiology, physiology and pharmacology. Experimental approach: A cDNA encoding for the Periplaneta americana 5-HT1 receptor was amplified from brain cDNA. The receptor was stably expressed in HEK 293 cells, and the functional and pharmacological properties were determined in cAMP assays. Receptor distribution was investigated by RT-PCR and by immunocytochemistry using an affinity-purified polyclonal antiserum. Key results: The P. americana 5-HT1 receptor (Pea5-HT1) shares pronounced sequence and functional similarity with mammalian 5-HT1 receptors. Activation with 5-HT reduced adenylyl cyclase activity in a dose-dependent manner. Pea5-HT1 was expressed as a constitutively active receptor with methiothepin acting as a neutral antagonist, and WAY 100635 as an inverse agonist. Receptor mRNA was present in various tissues including brain, salivary glands and midgut. Receptor-specific antibodies showed that the native protein was expressed in a glycosylated form in membrane samples of brain and salivary glands. Conclusions and implications: This study marks the first pharmacological identification of an inverse agonist and a neutral antagonist at an insect 5-HT1 receptor. The results presented here should facilitate further analyses of 5-HT1 receptors in mediating central and peripheral effects of 5-HT in insects.
KW - Biogenic amine
KW - constitutive activity
KW - cellular signalling
KW - G-protein-coupled receptor
KW - insect
Y1 - 2010
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44346
ER -
TY - GEN
A1 - Mooij, Wolf M.
A1 - Trolle, Dennis
A1 - Jeppesen, Erik
A1 - Arhonditsis, George B.
A1 - Belolipetsky, Pavel V.
A1 - Chitamwebwa, Deonatus B. R.
A1 - Degermendzhy, Andrey G.
A1 - DeAngelis, Donald L.
A1 - Domis, Lisette Nicole de Senerpont
A1 - Downing, Andrea S.
A1 - Elliott, J. Alex
A1 - Fragoso Jr., Carlos Ruberto
A1 - Gaedke, Ursula
A1 - Genova, Svetlana N.
A1 - Gulati, Ramesh D.
A1 - Håkanson, Lars
A1 - Hamilton, David P.
A1 - Hipsey, Matthew R.
A1 - ‘t Hoen, Jochem
A1 - Hülsmann, Stephan
A1 - Los, F. Hans
A1 - Makler-Pick, Vardit
A1 - Petzoldt, Thomas
A1 - Prokopkin, Igor G.
A1 - Rinke, Karsten
A1 - Schep, Sebastiaan A.
A1 - Tominaga, Koji
A1 - Van Dam, Anne A.
A1 - Van Nes, Egbert H.
A1 - Wells, Scott A.
A1 - Janse, Jan H.
T1 - Challenges and opportunities for integrating lake ecosystem modelling approaches
T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2 - A large number and wide variety of lake ecosystem models have been developed and published during the past four decades. We identify two challenges for making further progress in this field. One such challenge is to avoid developing more models largely following the concept of others ('reinventing the wheel'). The other challenge is to avoid focusing on only one type of model, while ignoring new and diverse approaches that have become available ('having tunnel vision'). In this paper, we aim at improving the awareness of existing models and knowledge of concurrent approaches in lake ecosystem modelling, without covering all possible model tools and avenues. First, we present a broad variety of modelling approaches. To illustrate these approaches, we give brief descriptions of rather arbitrarily selected sets of specific models. We deal with static models (steady state and regression models), complex dynamic models (CAEDYM, CE-QUAL-W2, Delft 3D-ECO, LakeMab, LakeWeb, MyLake, PCLake, PROTECH, SALMO), structurally dynamic models and minimal dynamic models. We also discuss a group of approaches that could all be classified as individual based: super-individual models (Piscator, Charisma), physiologically structured models, stage-structured models and traitbased models. We briefly mention genetic algorithms, neural networks, Kalman filters and fuzzy logic. Thereafter, we zoom in, as an in-depth example, on the multi-decadal development and application of the lake ecosystem model PCLake and related models (PCLake Metamodel, Lake Shira Model, IPH-TRIM3D-PCLake). In the discussion, we argue that while the historical development of each approach and model is understandable given its 'leading principle', there are many opportunities for combining approaches. We take the point of view that a single 'right' approach does not exist and should not be strived for. Instead, multiple modelling approaches, applied concurrently to a given problem, can help develop an integrative view on the functioning of lake ecosystems. We end with a set of specific recommendations that may be of help in the further development of lake ecosystem models.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1326
KW - aquatic
KW - food web dynamics
KW - plankton
KW - nutrients
KW - spatial
KW - lake
KW - freshwater
KW - marine
KW - community
KW - population
KW - hydrology
KW - eutrophication
KW - global change
KW - climate warming
KW - fisheries
KW - biodiversity
KW - management
KW - mitigation
KW - adaptive processes
KW - non-linear dynamics
KW - analysis
KW - bifurcation
KW - understanding
KW - prediction
KW - model limitations
KW - model integration
Y1 - 2010
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-429839
SN - 1866-8372
IS - 1326
ER -
TY - GEN
A1 - Dortay, Hakan
A1 - Müller-Röber, Bernd
T1 - A highly efficient pipeline for protein expression in Leishmania tarentolae sing infrared fluorescence protein as marker
N2 - Background: Leishmania tarentolae, a unicellular eukaryotic protozoan, has been established as a novel host for recombinant protein production in recent years. Current protocols for protein expression in Leishmania are, however, time consuming and require extensive lab work in order to identify well-expressing cell lines. Here we established an alternative protein expression work-flow that employs recently engineered infrared fluorescence protein (IFP) as a suitable and easy-to-handle reporter protein for recombinant protein expression in Leishmania. As model proteins we tested three proteins from the plant Arabidopsis thaliana, including a NAC and a type-B ARR transcription factor. Results: IFP and IFP fusion proteins were expressed in Leishmania and rapidly detected in cells by deconvolution microscopy and in culture by infrared imaging of 96-well microtiter plates using small cell culture volumes (2 μL - 100 μL). Motility, shape and growth of Leishmania cells were not impaired by intracellular accumulation of IFP. In-cell detection of IFP and IFP fusion proteins was straightforward already at the beginning of the expression pipeline and thus allowed early pre-selection of well-expressing Leishmania clones. Furthermore, IFP fusion proteins retained infrared fluorescence after electrophoresis in denaturing SDS-polyacrylamide gels, allowing direct in-gel detection without the need to disassemble cast protein gels. Thus, parameters for scaling up protein production and streamlining purification routes can be easily optimized when employing IFP as reporter. Conclusions: Using IFP as biosensor we devised a protocol for rapid and convenient protein expression in Leishmania tarentolae. Our expression pipeline is superior to previously established methods in that it significantly reduces the hands-on-time and work load required for identifying well-expressing clones, refining protein production parameters and establishing purification protocols. The facile in-cell and in-gel detection tools built on IFP make Leishmania amenable for high-throughput expression of proteins from plant and animal sources.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 122
KW - System
KW - Donovani
Y1 - 2010
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44773
ER -
TY - GEN
A1 - Bierbach, David
A1 - Schulte, Matthias
A1 - Herrmann, Nina
A1 - Tobler, Michael
A1 - Stadler, Stefan
A1 - Jung, Christian T.
A1 - Kunkel, Benjamin
A1 - Riesch, Rüdiger
A1 - Klaus, Sebastian
A1 - Ziege, Madlen
A1 - Indy, Jeane Rimber
A1 - Arias-Rodriguez, Lenin
A1 - Plath, Martin
T1 - Predator-induced changes of female mating preferences
BT - innate and experiential effects
T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2 - Background
In many species males face a higher predation risk than females because males display elaborate traits that evolved under sexual selection, which may attract not only females but also predators. Females are, therefore, predicted to avoid such conspicuous males under predation risk. The present study was designed to investigate predator-induced changes of female mating preferences in Atlantic mollies (Poecilia mexicana). Males of this species show a pronounced polymorphism in body size and coloration, and females prefer large, colorful males in the absence of predators.
Results
In dichotomous choice tests predator-naïve (lab-reared) females altered their initial preference for larger males in the presence of the cichlid Cichlasoma salvini, a natural predator of P. mexicana, and preferred small males instead. This effect was considerably weaker when females were confronted visually with the non-piscivorous cichlid Vieja bifasciata or the introduced non-piscivorous Nile tilapia (Oreochromis niloticus). In contrast, predator experienced (wild-caught) females did not respond to the same extent to the presence of a predator, most likely due to a learned ability to evaluate their predators' motivation to prey.
Conclusions
Our study highlights that (a) predatory fish can have a profound influence on the expression of mating preferences of their prey (thus potentially affecting the strength of sexual selection), and females may alter their mate choice behavior strategically to reduce their own exposure to predators. (b) Prey species can evolve visual predator recognition mechanisms and alter their mate choice only when a natural predator is present. (c) Finally, experiential effects can play an important role, and prey species may learn to evaluate the motivational state of their predators.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 984
KW - sexual selection
KW - female choice
KW - non-independent mate choice
KW - predator recognition
KW - Poecilia mexicana
Y1 - 2020
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431099
SN - 1866-8372
IS - 984
ER -
TY - GEN
A1 - Eccard, Jana
A1 - Fey, Karen
A1 - Caspers, Barbara A.
A1 - Ylönen, Hannu
T1 - Breeding state and season affect interspecific interaction types
BT - indirect resource competition and direct interference
T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe
N2 - Indirect resource competition and interference are widely occurring mechanisms of interspecific interactions. We have studied the seasonal expression of these two interaction types within a two-species, boreal small mammal system. Seasons differ by resource availability, individual breeding state and intraspecific social system. Live-trapping methods were used to monitor space use and reproduction in 14 experimental populations of bank voles Myodes glareolus in large outdoor enclosures with and without a dominant competitor, the field vole Microtus agrestis. We further compared vole behaviour using staged dyadic encounters in neutral arenas in both seasons. Survival of the non-breeding overwintering bank voles was not affected by competition. In the spring, the numbers of male bank voles, but not of females, were reduced significantly in the competition populations. Bank vole home ranges expanded with vole density in the presence of competitors, indicating food limitation. A comparison of behaviour between seasons based on an analysis of similarity revealed an avoidance of costly aggression against opponents, independent of species. Interactions were more aggressive during the summer than during the winter, and heterospecific encounters were more aggressive than conspecific encounters. Based on these results, we suggest that interaction types and their respective mechanisms are not either–or categories and may change over the seasons. During the winter, energy constraints and thermoregulatory needs decrease direct aggression, but food constraints increase indirect resource competition. Direct interference appears in the summer, probably triggered by each individual’s reproductive and hormonal state and the defence of offspring against conspecific and heterospecific intruders. Both interaction forms overlap in the spring, possibly contributing to spring declines in the numbers of subordinate species.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 729
KW - rodents
KW - aggression
KW - seasonality
KW - space use
KW - winter biology
Y1 - 2019
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-429398
SN - 1866-8372
IS - 729
SP - 623
EP - 633
ER -
TY - GEN
A1 - Breitenstein, Michael
A1 - Nielsen, Peter E.
A1 - Hölzel, Ralph
A1 - Bier, Frank Fabian
T1 - DNA-nanostructure-assembly by sequential spotting
T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2 - Background: The ability to create nanostructures with biomolecules is one of the key elements in nanobiotechnology. One of the problems is the expensive and mostly custom made equipment which is needed for their development. We intended to reduce material costs and aimed at miniaturization of the necessary tools that are essential for nanofabrication. Thus we combined the capabilities of molecular ink lithography with DNA-self-assembling capabilities to arrange DNA in an independent array which allows addressing molecules in nanoscale dimensions.
Results: For the construction of DNA based nanostructures a method is presented that allows an arrangement of DNA strands in such a way that they can form a grid that only depends on the spotted pattern of the anchor molecules. An atomic force microscope (AFM) has been used for molecular ink lithography to generate small spots. The sequential spotting process allows the immobilization of several different functional biomolecules with a single AFM-tip. This grid which delivers specific addresses for the prepared DNA-strand serves as a two-dimensional anchor to arrange the sequence according to the pattern. Once the DNA-nanoarray has been formed, it can be functionalized by PNA (peptide nucleic acid) to incorporate advanced structures.
Conclusions: The production of DNA-nanoarrays is a promising task for nanobiotechnology. The described method allows convenient and low cost preparation of nanoarrays. PNA can be used for complex functionalization purposes as well as a structural element.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1027
KW - atomic force microscope
KW - peptide nucleic acid
KW - persistence length
KW - adapter oligonucleotide
KW - high fluorescence signal
Y1 - 2020
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431108
SN - 1866-8372
IS - 1027
ER -
TY - GEN
A1 - Baumann, Tobias
A1 - Arndt, Katja Maren
A1 - Müller, Kristian M.
T1 - Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V
T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2 - Background: DNA fragments carrying internal recognition sites for the restriction endonucleases intended for cloning into a target plasmid pose a challenge for conventional cloning.
Results: A method for directional insertion of DNA fragments into plasmid vectors has been developed. The target sequence is amplified from a template DNA sample by PCR using two oligonucleotides each containing a single deoxyinosine base at the third position from the 5' end. Treatment of such PCR products with endonuclease V generates 3' protruding ends suitable for ligation with vector fragments created by conventional restriction endonuclease reactions.
Conclusions: The developed approach generates terminal cohesive ends without the use of Type II restriction endonucleases, and is thus independent from the DNA sequence. Due to PCR amplification, minimal amounts of template DNA are required. Using the robust Taq enzyme or a proofreading Pfu DNA polymerase mutant, the method is applicable to a broad range of insert sequences. Appropriate primer design enables direct incorporation of terminal DNA sequence modifications such as tag addition, insertions, deletions and mutations into the cloning strategy. Further, the restriction sites of the target plasmid can be either retained or removed.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 983
KW - cohesive ends
KW - DNA cleavage
KW - genetic vectors
KW - modified primers
KW - molecular methods
KW - polymerase chain reaction
KW - recombinant Escherichia coli
KW - restriction enzymes
Y1 - 2020
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431085
SN - 1866-8372
IS - 983
ER -
TY - GEN
A1 - Pavesi, Laura
A1 - Tiedemann, Ralph
A1 - De Matthaeis, Elvira
A1 - Ketmaier, Valerio
T1 - Genetic connectivity between land and sea
BT - the case of the beachflea Orchestia montagui (Crustacea, Amphipoda, Talitridae) in the Mediterranean Sea
N2 - Introduction: We examined patterns of genetic divergence in 26 Mediterranean populations of the semi-terrestrial beachflea Orchestia montagui using mitochondrial (cytochrome oxidase subunit I), microsatellite (eight loci) and allozymic data. The species typically forms large populations within heaps of dead seagrass leaves stranded on beaches at the waterfront. We adopted a hierarchical geographic sampling to unravel population structure in a species living at the sea-land transition and, hence, likely subjected to dramatically contrasting forces.
Results: Mitochondrial DNA showed historical phylogeographic breaks among Adriatic, Ionian and the remaining basins (Tyrrhenian, Western and Eastern Mediterranean Sea) likely caused by the geological and climatic changes of the Pleistocene. Microsatellites (and to a lesser extent allozymes) detected a further subdivision between and within the Western Mediterranean and the Tyrrhenian Sea due to present-day processes. A pattern of isolation by distance was not detected in any of the analyzed data set.
Conclusions: We conclude that the population structure of O. montagui is the result of the interplay of two contrasting forces that act on the species population genetic structure. On one hand, the species semi-terrestrial life style would tend to determine the onset of local differences. On the other hand, these differences are partially counter-balanced by passive movements of migrants via rafting on heaps of dead seagrass leaves across sites by sea surface currents. Approximate Bayesian Computations support dispersal at sea as prevalent over terrestrial regionalism.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 399
KW - Orchestia montagui
KW - Talitrids
KW - Mediterranean Sea
KW - Phylogeography
KW - Mitochondrial DNA
KW - Microsatellites
KW - Allozymes
KW - Approximate Bayesian Computation
Y1 - 2017
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-401110
ER -
TY - GEN
A1 - Schwarte, Sandra
A1 - Brust, Henrike
A1 - Steup, Martin
A1 - Tiedemann, Ralph
T1 - Intraspecific sequence variation and differential expression in starch synthase genes of Arabidopsis thaliana
T2 - BMC Research Notes
N2 - Background
Natural accessions of Arabidopsis thaliana are a well-known system to measure levels of intraspecific genetic variation. Leaf starch content correlates negatively with biomass. Starch is synthesized by the coordinated action of many (iso)enzymes. Quantitatively dominant is the repetitive transfer of glucosyl residues to the non-reducing ends of α-glucans as mediated by starch synthases. In the genome of A. thaliana, there are five classes of starch synthases, designated as soluble starch synthases (SSI, SSII, SSIII, and SSIV) and granule-bound synthase (GBSS). Each class is represented by a single gene. The five genes are homologous in functional domains due to their common origin, but have evolved individual features as well. Here, we analyze the extent of genetic variation in these fundamental protein classes as well as possible functional implications on transcript and protein levels.
Findings
Intraspecific sequence variation of the five starch synthases was determined by sequencing the entire loci including promoter regions from 30 worldwide distributed accessions of A. thaliana. In all genes, a considerable number of nucleotide polymorphisms was observed, both in non-coding and coding regions, and several amino acid substitutions were identified in functional domains. Furthermore, promoters possess numerous polymorphisms in potentially regulatory cis-acting regions. By realtime experiments performed with selected accessions, we demonstrate that DNA sequence divergence correlates with significant differences in transcript levels.
Conclusions
Except for AtSSII, all starch synthase classes clustered into two or three groups of haplotypes, respectively. Significant difference in transcript levels among haplotype clusters in AtSSIV provides evidence for cis-regulation. By contrast, no such correlation was found for AtSSI, AtSSII, AtSSIII, and AtGBSS, suggesting trans-regulation. The expression data presented here point to a regulation by common trans-regulatory transcription factors which ensures a coordinated action of the products of these four genes during starch granule biosynthesis. The apparent cis-regulation of AtSSIV might be related to its role in the initiation of de novo biosynthesis of granules.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 400
KW - Arabidopsis thaliana
KW - starch synthases
KW - genetic variation
KW - transcript level
Y1 - 2017
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-401128
ER -
TY - GEN
A1 - Eccard, Jana
A1 - Herde, Antje
T1 - Seasonal variation in the behaviour of a short-lived rodent
N2 - Background: Short lived, iteroparous animals in seasonal environments experience variable social and environmental conditions over their lifetime. Animals can be divided into those with a "young-of-the-year" life history (YY, reproducing and dying in the summer of birth) and an "overwinter" life history (OW, overwintering in a subadult state before reproducing next spring).
We investigated how behavioural patterns across the population were affected by season and sex, and whether variation in behaviour reflects the variation in life history patterns of each season. Applications of pace-of-life (POL) theory would suggest that long-lived OW animals are shyer in order to increase survival, and YY are bolder in order to increase reproduction. Therefore, we expected that in winter and spring samples, when only OW can be sampled, the animals should be shyer than in summer and autumn, when both OW and YY animals can be sampled. We studied common vole (Microtus arvalis) populations, which express typical, intra-annual density fluctuation. We captured a total of 492 voles at different months over 3 years and examined boldness and activity level with two standardised behavioural experiments.
Results: Behavioural variables of the two tests were correlated with each other. Boldness, measured as short latencies in both tests, was extremely high in spring compared to other seasons. Activity level was highest in spring and summer, and higher in males than in females.
Conclusion: Being bold in laboratory tests may translate into higher risk-taking in nature by being more mobile while seeking out partners or valuable territories. Possible explanations include asset-protection, with OW animals being rather old with low residual reproductive value in spring. Therefore, OW may take higher risks during this season. Offspring born in spring encounter a lower population density and may have higher reproductive value than offspring of later cohorts. A constant connection between life history and animal personality, as suggested by the POL theory, however, was not found. Nevertheless, correlations of traits suggest the existence of animal personalities. In conclusion, complex patterns of population dynamics, seasonal variation in life histories, and variability of behaviour due to asset-protection may cause complex seasonal behavioural dynamics in a population.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 403
KW - animal personalities
KW - boldness
KW - life history
KW - pace-of-life
KW - POL
KW - phenotypic plasticity
KW - common vole
Y1 - 2017
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-401370
ER -
TY - GEN
A1 - Jeltsch, Florian
A1 - Bonte, Dries
A1 - Pe'er, Guy
A1 - Reineking, Björn
A1 - Leimgruber, Peter
A1 - Balkenhol, Niko
A1 - Schröder-Esselbach, Boris
A1 - Buchmann, Carsten M.
A1 - Müller, Thomas
A1 - Blaum, Niels
A1 - Zurell, Damaris
A1 - Böhning-Gaese, Katrin
A1 - Wiegand, Thorsten
A1 - Eccard, Jana
A1 - Hofer, Heribert
A1 - Reeg, Jette
A1 - Eggers, Ute
A1 - Bauer, Silke
T1 - Integrating movement ecology with biodiversity research
BT - exploring new avenues to address spatiotemporal biodiversity dynamics
N2 - Movement of organisms is one of the key mechanisms shaping biodiversity, e.g. the distribution of genes, individuals and species in space and time. Recent technological and conceptual advances have improved our ability to assess the causes and consequences of individual movement, and led to the emergence of the new field of ‘movement ecology’. Here, we outline how movement ecology can contribute to the broad field of biodiversity research, i.e. the study of processes and patterns of life among and across different scales, from genes to ecosystems, and we propose a conceptual framework linking these hitherto largely separated fields of research. Our framework builds on the concept of movement ecology for individuals, and demonstrates its importance for linking individual organismal movement with biodiversity. First, organismal movements can provide ‘mobile links’ between habitats or ecosystems, thereby connecting resources, genes, and processes among otherwise separate locations. Understanding these mobile links and their impact on biodiversity will be facilitated by movement ecology, because mobile links can be created by different modes of movement (i.e., foraging, dispersal, migration) that relate to different spatiotemporal scales and have differential effects on biodiversity. Second, organismal movements can also mediate coexistence in communities, through ‘equalizing’ and ‘stabilizing’ mechanisms. This novel integrated framework provides a conceptual starting point for a better understanding of biodiversity dynamics in light of individual movement and space-use behavior across spatiotemporal scales. By illustrating this framework with examples, we argue that the integration of movement ecology and biodiversity research will also enhance our ability to conserve diversity at the genetic, species, and ecosystem levels.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 401
KW - mobile links
KW - species coexistence
KW - community dynamics
KW - biodiversity conservation
KW - long distance movement
KW - landscape genetics
KW - individual based modeling
Y1 - 2017
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-401177
ER -
TY - GEN
A1 - Liesenjohann, Monique
A1 - Liesenjohann, Thilo
A1 - Palme, Rupert
A1 - Eccard, Jana
T1 - Differential behavioural and endocrine responses of common voles (Microtus arvalis) to nest predators and resource competitors
N2 - Background: Adaptive behavioural strategies promoting co-occurrence of competing species are known to result from a sympatric evolutionary past. Strategies should be different for indirect resource competition (exploitation, e.g., foraging and avoidance behaviour) than for direct interspecific interference (e.g., aggression, vigilance, and nest guarding). We studied the effects of resource competition and nest predation in sympatric small mammal species using semi-fossorial voles and shrews, which prey on vole offspring during their sensitive nestling phase. Experiments were conducted in caged outdoor enclosures. Focus common vole mothers (Microtus arvalis) were either caged with a greater white-toothed shrew (Crocidura russula) as a potential nest predator, with an herbivorous field vole (Microtus agrestis) as a heterospecific resource competitor, or with a conspecific resource competitor.
Results: We studied behavioural adaptations of vole mothers during pregnancy, parturition, and early lactation, specifically modifications of the burrow architecture and activity at burrow entrances. Further, we measured pre- and postpartum faecal corticosterone metabolites (FCMs) of mothers to test for elevated stress hormone levels. Only in the presence of the nest predator were prepartum FCMs elevated, but we found no loss of vole nestlings and no differences in nestling body weight in the presence of the nest predator or the heterospecific resource competitor. Although the presence of both the shrew and the field vole induced prepartum modifications to the burrow architecture, only nest predators caused an increase in vigilance time at burrow entrances during the sensitive nestling phase.
Conclusion: Voles displayed an adequate behavioural response for both resource competitors and nest predators. They modified burrow architecture to improve nest guarding and increased their vigilance at burrow entrances to enhance offspring survival chances. Our study revealed differential behavioural adaptations to resource competitors and nest predators.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 402
KW - behavioural adaptations
KW - small mammals
KW - interspecific interactions
KW - nest predation
KW - stress response
KW - faecal corticosterone metabolites
KW - burrow system
KW - shrews
KW - voles
Y1 - 2017
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-401184
ER -
TY - GEN
A1 - Badalyan, Artavazd
A1 - Dierich, Marlen
A1 - Stiba, Konstanze
A1 - Schwuchow, Viola
A1 - Leimkühler, Silke
A1 - Wollenberger, Ulla
T1 - Electrical wiring of the aldehyde oxidoreductase PaoABC with a polymer containing osmium redox centers
BT - biosensors for benzaldehyde and GABA
T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2 - Biosensors for the detection of benzaldehyde and g-aminobutyric acid (GABA) are reported using aldehyde oxidoreductase PaoABC from Escherichia coli immobilized in a polymer containing bound low potential osmium redox complexes. The electrically connected enzyme already electrooxidizes benzaldehyde at potentials below −0.15 V (vs. Ag|AgCl, 1 M KCl). The pH-dependence of benzaldehyde oxidation can be strongly influenced by the ionic strength. The effect is similar with the soluble osmium redox complex and therefore indicates a clear electrostatic effect on the bioelectrocatalytic efficiency of PaoABC in the osmium containing redox polymer. At lower ionic strength, the pH-optimum is high and can be switched to low pH-values at high ionic strength. This offers biosensing at high and low pH-values. A “reagentless” biosensor has been formed with enzyme wired onto a screen-printed electrode in a flow cell device. The response time to addition of benzaldehyde is 30 s, and the measuring range is between 10–150 µM and the detection limit of 5 µM (signal to noise ratio 3:1) of benzaldehyde. The relative standard deviation in a series (n = 13) for 200 µM benzaldehyde is 1.9%. For the biosensor, a response to succinic semialdehyde was also identified. Based on this response and the ability to work at high pH a biosensor for GABA is proposed by coimmobilizing GABA-aminotransferase (GABA-T) and PaoABC in the osmium containing redox polymer.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1082
KW - redox polymer
KW - aldehyde oxidoreductase
KW - ionic strength
KW - benzaldehyde
KW - GABA
KW - biosensor
Y1 - 2021
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-475070
SN - 1866-8372
IS - 1082
ER -
TY - GEN
A1 - Huynen, Leon
A1 - Suzuki, Takayuki
A1 - Ogura, Toshihiko
A1 - Watanabe, Yusuke
A1 - Millar, Craig D.
A1 - Hofreiter, Michael
A1 - Smith, Craig
A1 - Mirmoeini, Sara
A1 - Lambert, David M.
T1 - Reconstruction and in vivo analysis of the extinct tbx5 gene from ancient wingless moa (Aves: Dinornithiformes)
T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2 - Background
The forelimb-specific gene tbx5 is highly conserved and essential for the development of forelimbs in zebrafish, mice, and humans. Amongst birds, a single order, Dinornithiformes, comprising the extinct wingless moa of New Zealand, are unique in having no skeletal evidence of forelimb-like structures.
Results
To determine the sequence of tbx5 in moa, we used a range of PCR-based techniques on ancient DNA to retrieve all nine tbx5 exons and splice sites from the giant moa, Dinornis. Moa Tbx5 is identical to chicken Tbx5 in being able to activate the downstream promotors of fgf10 and ANF. In addition we show that missexpression of moa tbx5 in the hindlimb of chicken embryos results in the formation of forelimb features, suggesting that Tbx5 was fully functional in wingless moa. An alternatively spliced exon 1 for tbx5 that is expressed specifically in the forelimb region was shown to be almost identical between moa and ostrich, suggesting that, as well as being fully functional, tbx5 is likely to have been expressed normally in moa since divergence from their flighted ancestors, approximately 60 mya.
Conclusions
The results suggests that, as in mice, moa tbx5 is necessary for the induction of forelimbs, but is not sufficient for their outgrowth. Moa Tbx5 may have played an important role in the development of moa’s remnant forelimb girdle, and may be required for the formation of this structure. Our results further show that genetic changes affecting genes other than tbx5 must be responsible for the complete loss of forelimbs in moa.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1117
KW - tbx5
KW - Moa
KW - gene expression
KW - ancient DNA
KW - development
KW - forelimb
Y1 - 2021
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431599
SN - 1866-8372
IS - 1117
ER -
TY - GEN
A1 - Yarman, Aysu
A1 - Scheller, Frieder W.
T1 - The first electrochemical MIP sensor for tamoxifen
T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2 - We present an electrochemical MIP sensor for tamoxifen (TAM)-a nonsteroidal anti-estrogen-which is based on the electropolymerisation of an O-phenylenediamine. resorcinol mixture directly on the electrode surface in the presence of the template molecule. Up to now only. bulk. MIPs for TAM have been described in literature, which are applied for separation in chromatography columns. Electro-polymerisation of the monomers in the presence of TAM generated a film which completely suppressed the reduction of ferricyanide. Removal of the template gave a markedly increased ferricyanide signal, which was again suppressed after rebinding as expected for filling of the cavities by target binding. The decrease of the ferricyanide peak of the MIP electrode depended linearly on the TAM concentration between 1 and 100 nM. The TAM-imprinted electrode showed a 2.3 times higher recognition of the template molecule itself as compared to its metabolite 4-hydroxytamoxifen and no cross-reactivity with the anticancer drug doxorubucin was found. Measurements at + 1.1 V caused a fouling of the electrode surface, whilst pretreatment of TAM with peroxide in presence of HRP generated an oxidation product which was reducible at 0 mV, thus circumventing the polymer formation and electrochemical interferences.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1046
KW - molecularly imprinted polymers
KW - anticancer drug
KW - tamoxifen
KW - electropolymerisation
Y1 - 2020
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-476173
SN - 1866-8372
IS - 1046
ER -
TY - GEN
A1 - Gamba, Cristina
A1 - Jones, Eppie R.
A1 - Teasdale, Matthew D.
A1 - McLaughlin, Russell L.
A1 - González-Fortes, Gloria M.
A1 - Mattiangeli, Valeria
A1 - Domboróczki, László
A1 - Kővári, Ivett
A1 - Pap, Ildikó
A1 - Anders, Alexandra
A1 - Whittle, Alasdair
A1 - Dani, János
A1 - Raczky, Pál
A1 - Higham, Thomas F. G.
A1 - Hofreiter, Michael
A1 - Bradley, Daniel G.
A1 - Pinhasi, Ron
T1 - Genome flux and stasis in a five millennium transect of European prehistory
T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2 - The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (similar to 22x) and seven to similar to 1x coverage, to investigate the impact of these on Europe's genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1332
KW - ancient DNA
KW - lactase-persistence
KW - positive selection
KW - patterns
KW - sequence
KW - farmers
KW - pigmentation
KW - homozygosity
KW - ancestry
KW - skin
Y1 - 2014
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-437999
SN - 1866-8372
VL - 5
IS - 1332
ER -
TY - GEN
A1 - Schedina, Ina Maria
A1 - Hartmann, Stefanie
A1 - Groth, Detlef
A1 - Schlupp, Ingo
A1 - Tiedemann, Ralph
T1 - Comparative analysis of the gonadal transcriptomes of the all-female species Poecilia formosa and its maternal ancestor Poecilia mexicana
N2 - Background
The Amazon molly, Poecilia formosa (Teleostei: Poeciliinae) is an unisexual, all-female species. It evolved through the hybridisation of two closely related sexual species and exhibits clonal reproduction by sperm dependent parthenogenesis (or gynogenesis) where the sperm of a parental species is only used to activate embryogenesis of the apomictic, diploid eggs but does not contribute genetic material to the offspring.
Here we provide and describe the first de novo assembled transcriptome of the Amazon molly in comparison with its maternal ancestor, the Atlantic molly Poecilia mexicana. The transcriptome data were produced through sequencing of single end libraries (100 bp) with the Illumina sequencing technique.
Results
83,504,382 reads for the Amazon molly and 81,625,840 for the Atlantic molly were assembled into 127,283 and 78,961 contigs for the Amazon molly and the Atlantic molly, respectively. 63% resp. 57% of the contigs could be annotated with gene ontology terms after sequence similarity comparisons. Furthermore, we were able to identify genes normally involved in reproduction and especially in meiosis also in the transcriptome dataset of the apomictic reproducing Amazon molly.
Conclusions
We assembled and annotated the transcriptome of a non-model organism, the Amazon molly, without a reference genome (de novo). The obtained dataset is a fundamental resource for future research in functional and expression analysis. Also, the presence of 30 meiosis-specific genes within a species where no meiosis is known to take place is remarkable and raises new questions for future research.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 404
Y1 - 2017
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-401420
ER -
TY - GEN
A1 - Azuma, Yusuke
A1 - Kükenshöner, Tim
A1 - Ma, Guangyong
A1 - Yasunaga, Jun-ichiro
A1 - Imanishi, Miki
A1 - Tanaka, Gen
A1 - Nakase, Ikuhiko
A1 - Maruno, Takahiro
A1 - Kobayashi, Yuji
A1 - Arndt, Katja Maren
A1 - Matsuoka, Masao
A1 - Futaki, Shiroh
T1 - Controlling leucine-zipper partner recognition in cells through modification of a–g interactions
N2 - By focusing on the a–g interactions, successful design and selection were accomplished to obtain a leucine-zipper segment that discriminates the appropriate partner over another that provides very similar patterns of electrostatic interactions.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 276
Y1 - 2016
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-98758
ER -
TY - GEN
A1 - Zór, K.
A1 - Heiskanen, A.
A1 - Caviglia, Claudia
A1 - Vergani, M.
A1 - Landini, E.
A1 - Shah, F.
A1 - Carminati, Marco
A1 - Martínez-Serrano, A.
A1 - Ramos Moreno, T.
A1 - Kokaia, M.
A1 - Benayahu, Dafna
A1 - Keresztes, Zs.
A1 - Papkovsky, D.
A1 - Wollenberger, Ursula
A1 - Svendsen, W. E.
A1 - Dimaki, M.
A1 - Ferrari, G.
A1 - Raiteri, R.
A1 - Sampietro, M.
A1 - Dufva, M.
A1 - Emnéus, J.
T1 - A compact multifunctional microfluidic platform for exploring cellular dynamics in real-time using electrochemical detection
N2 - Downscaling of microfluidic cell culture and detection devices for electrochemical monitoring has mostly focused on miniaturization of the microfluidic chips which are often designed for specific applications and therefore lack functional flexibility. We present a compact microfluidic cell culture and electrochemical analysis platform with in-built fluid handling and detection, enabling complete cell based assays comprising on-line electrode cleaning, sterilization, surface functionalization, cell seeding, cultivation and electrochemical real-time monitoring of cellular dynamics. To demonstrate the versatility and multifunctionality of the platform, we explored amperometric monitoring of intracellular redox activity in yeast (Saccharomyces cerevisiae) and detection of exocytotically released dopamine from rat pheochromocytoma cells (PC12). Electrochemical impedance spectroscopy was used in both applications for monitoring cell sedimentation and adhesion as well as proliferation in the case of PC12 cells. The influence of flow rate on the signal amplitude in the detection of redox metabolism as well as the effect of mechanical stimulation on dopamine release were demonstrated using the programmable fluid handling capability. The here presented platform is aimed at applications utilizing cell based assays, ranging from e.g. monitoring of drug effects in pharmacological studies, characterization of neural stem cell differentiation, and screening of genetically modified microorganisms to environmental monitoring.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 289
Y1 - 2014
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-99492
ER -
TY - GEN
A1 - Bechi, Beatrice
A1 - Herter, Susanne
A1 - McKenna, Shane
A1 - Riley, Christopher
A1 - Leimkühler, Silke
A1 - Turner, Nicholas J.
A1 - Carnell, Andrew J.
T1 - Catalytic bio–chemo and bio–bio tandem oxidation reactions for amide and carboxylic acid synthesis
N2 - A catalytic toolbox for three different water-based one-pot cascades to convert aryl alcohols to amides and acids and cyclic amines to lactams, involving combination of oxidative enzymes (monoamine oxidase, xanthine dehydrogenase, galactose oxidase and laccase) and chemical oxidants (TBHP or CuI(cat)/H2O2) at mild temperatures, is presented. Mutually compatible conditions were found to afford products in good to excellent yields.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 282
Y1 - 2014
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-99414
ER -
TY - GEN
A1 - Pajoro, Alice
A1 - Madrigal, Pedro
A1 - Muiño, Jose M.
A1 - Matus, José Tomás
A1 - Jin, Jian
A1 - Mecchia, Martin A.
A1 - Debernardi, Juan M.
A1 - Palatnik, Javier F.
A1 - Balazadeh, Salma
A1 - Arif, Muhammad
A1 - Ó’Maoiléidigh, Diarmuid S.
A1 - Wellmer, Frank
A1 - Krajewski, Pawel
A1 - Riechmann, José-Luis
A1 - Angenent, Gerco C.
A1 - Kaufmann, Kerstin
T1 - Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2 - Background: Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood.
Results: We characterized the relationship of chromatin accessibility, gene expression, and DNA binding of two MADS-domain proteins at different stages of Arabidopsis flower development. Dynamic changes in APETALA1 and SEPALLATA3 DNA binding correlated with changes in gene expression, and many of the target genes could be associated with the developmental stage in which they are transcriptionally controlled. We also observe dynamic changes in chromatin accessibility during flower development. Remarkably, DNA binding of APETALA1 and SEPALLATA3 is largely independent of the accessibility status of their binding regions and it can precede increases in DNA accessibility. These results suggest that APETALA1 and SEPALLATA3 may modulate chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes.
Conclusions: Our findings indicate that different homeotic factors regulate partly overlapping, yet also distinctive sets of target genes in a partly stage-specific fashion. By combining the information from DNA-binding and gene expression data, we are able to propose models of stage-specific regulatory interactions, thereby addressing dynamics of regulatory networks throughout flower development. Furthermore, MADS-domain TFs may regulate gene expression by alternative strategies, one of which is modulation of chromatin accessibility.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1327
KW - flower development
KW - floral organ
KW - floral meristem
KW - chromatin accessibility
KW - growth regulate factor
Y1 - 2014
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431139
SN - 1866-8372
VL - 15
ER -
TY - GEN
A1 - Valente, Luis M.
A1 - Phillimore, Albert B.
A1 - Etienne, Rampal S.
T1 - Equilibrium and non-equilibrium dynamics simultaneously operate in the Galápagos islands
N2 - Island biotas emerge from the interplay between colonisation, speciation and extinction and are often the scene of spectacular adaptive radiations. A common assumption is that insular diversity is at a dynamic equilibrium, but for remote islands, such as Hawaii or Galápagos, this idea remains untested. Here, we reconstruct the temporal accumulation of terrestrial bird species of the Galápagos using a novel phylogenetic method that estimates rates of biota assembly for an entire community. We show that species richness on the archipelago is in an ascending phase and does not tend towards equilibrium. The majority of the avifauna diversifies at a slow rate, without detectable ecological limits. However, Darwin's finches form an exception: they rapidly reach a carrying capacity and subsequently follow a coalescent-like diversification process. Together, these results suggest that avian diversity of remote islands is rising, and challenge the mutual exclusivity of the non-equilibrium and equilibrium ecological paradigms.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 230
KW - Community assembly
KW - diversification
KW - dynamic equilibrium
KW - island biogeography
KW - phylogeny
Y1 - 2015
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-93525
ER -
TY - GEN
A1 - Muiño, Jose M.
A1 - de Bruijn, Suzanne
A1 - Pajoro, Alice
A1 - Geuten, Koen
A1 - Vingron, Martin
A1 - Angenent, Gerco C.
A1 - Kaufmann, Kerstin
T1 - Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor
N2 - Flower development is controlled by the action of key regulatory transcription factors of the MADS-domain family. The function of these factors appears to be highly conserved among species based on mutant phenotypes. However, the conservation of their downstream processes is much less well understood, mostly because the evolutionary turnover and variation of their DNA-binding sites (BSs) among plant species have not yet been experimentally determined. Here, we performed comparative ChIP (chromatin immunoprecipitation)-seq experiments of the MADS-domain transcription factor SEPALLATA3 (SEP3) in two closely related Arabidopsis species: Arabidopsis thaliana and A. lyrata which have very similar floral organ morphology. We found that BS conservation is associated with DNA sequence conservation, the presence of the CArG-box BS motif and on the relative position of the BS to its potential target gene. Differences in genome size and structure can explain that SEP3 BSs in A. lyrata can be located more distantly to their potential target genes than their counterparts in A. thaliana. In A. lyrata, we identified transposition as a mechanism to generate novel SEP3 binding locations in the genome. Comparative gene expression analysis shows that the loss/gain of BSs is associated with a change in gene expression. In summary, this study investigates the evolutionary dynamics of DNA BSs of a floral key-regulatory transcription factor and explores factors affecting this phenomenon.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 261
KW - MADS-domain transcription factor
KW - cis-regulatory evolution
KW - plant development
Y1 - 2015
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-96580
SP - 1225
EP - 1245
ER -
TY - GEN
A1 - McKenna, Shane M.
A1 - Leimkühler, Silke
A1 - Herter, Susanne
A1 - Turner, Nicholas J.
A1 - Carnell, Andrew J.
T1 - Enzyme cascade reactions
BT - synthesis of furandicarboxylic acid (FDCA) and carboxylic acids using oxidases in tandem
N2 - A one-pot tandem enzyme reaction using galactose oxidase M3–5 and aldehyde oxidase PaoABC was used to convert hydroxymethylfurfural (HMF) to the pure bioplastics precursor FDCA in 74% isolated yield. A range of alcohols was also converted to carboxylic acids in high yield under mild conditions.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 300
Y1 - 2015
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-102271
SP - 3271
EP - 3275
ER -
TY - GEN
A1 - Lamanna, Francesco
A1 - Kirschbaum, Frank
A1 - Waurick, Isabelle
A1 - Dieterich, Christoph
A1 - Tiedemann, Ralph
T1 - Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae)
N2 - Background African weakly-electric fishes of the family Mormyridae are able to produce and perceive weak electric signals (typically less than one volt in amplitude) owing to the presence of a specialized, muscle-derived electric organ (EO) in their tail region. Such electric signals, also known as Electric Organ Discharges (EODs), are used for objects/prey localization, for the identification of conspecifics, and in social and reproductive behaviour. This feature might have promoted the adaptive radiation of this family by acting as an effective pre-zygotic isolation mechanism. Despite the physiological and evolutionary importance of this trait, the investigation of the genetic basis of its function and modification has so far remained limited. In this study, we aim at: i) identifying constitutive differences in terms of gene expression between electric organ and skeletal muscle (SM) in two mormyrid species of the genus Campylomormyrus: C. compressirostris and C. tshokwe, and ii) exploring cross-specific patterns of gene expression within the two tissues among C. compressirostris, C. tshokwe, and the outgroup species Gnathonemus petersii. Results Twelve paired-end (100 bp) strand-specific RNA-seq Illumina libraries were sequenced, producing circa 330 M quality-filtered short read pairs. The obtained reads were assembled de novo into four reference transcriptomes. In silico cross-tissue DE-analysis allowed us to identify 271 shared differentially expressed genes between EO and SM in C. compressirostris and C.tshokwe. Many of these genes correspond to myogenic factors, ion channels and pumps, and genes involved in several metabolic pathways. Cross-species analysis has revealed that the electric organ transcriptome is more variable in terms of gene expression levels across species than the skeletal muscle transcriptome. Conclusions The data obtained indicate that: i) the loss of contractile activity and the decoupling of the excitation-contraction processes are reflected by the down-regulation of the corresponding genes in the electric organ’s transcriptome; ii) the metabolic activity of the EO might be specialized towards the production and turn-over of membrane structures; iii) several ion channels are highly expressed in the EO in order to increase excitability; iv) several myogenic factors might be down-regulated by transcription repressors in the EO.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 212
Y1 - 2015
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-86997
ER -
TY - GEN
A1 - Sbragaglia, Valerio
A1 - Lamanna, Francesco
A1 - Mat, Audrey M.
A1 - Rotllant, Guiomar
A1 - Joly, Silvia
A1 - Ketmaier, Valerio
A1 - de la Iglesia, Horacio O.
A1 - Aguzzi, Jacopo
T1 - Identification, Characterization, and Diel Pattern of Expression of Canonical Clock Genes in Nephrops norvegicus (Crustacea: Decapoda) Eyestalk
N2 - The Norway lobster, Nephrops norvegicus, is a burrowing decapod with a rhythmic burrow emergence (24 h) governed by the circadian system. It is an important resource for European fisheries and its behavior deeply affects its availability. The current knowledge of Nephrops circadian biology is phenomenological as it is currently the case for almost all crustaceans. In attempt to elucidate the putative molecular mechanisms underlying circadian gene regulation in Nephrops, we used a transcriptomics approach on cDNA extracted from the eyestalk, a structure playing a crucial role in controlling behavior of decapods. We studied 14 male lobsters under 12–12 light-darkness blue light cycle. We used the Hiseq 2000 Illumina platform to sequence two eyestalk libraries (under light and darkness conditions) obtaining about 90 millions 100-bp paired-end reads. Trinity was used for the de novo reconstruction of transcriptomes; the size at which half of all assembled bases reside in contigs (N50) was equal to 1796 (light) and 2055 (darkness). We found a list of candidate clock genes and focused our attention on canonical ones: timeless, period, clock and bmal1. The cloning of assembled fragments validated Trinity outputs. The putative Nephrops clock genes showed high levels of identity (blastx on NCBI) with known crustacean clock gene homologs such as Eurydice pulchra (period: 47%, timeless: 59%, bmal1: 79%) and Macrobrachium rosenbergii (clock: 100%). We also found a vertebrate-like cryptochrome 2. RT-qPCR showed that only timeless had a robust diel pattern of expression. Our data are in accordance with the current knowledge of the crustacean circadian clock, reinforcing the idea that the molecular clockwork of this group shows some differences with the established model in Drosophila melanogaster.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 205
Y1 - 2015
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-84432
ER -
TY - GEN
A1 - Kehr, Jan-Christoph
A1 - Dittmann-Thünemann, Elke
T1 - Biosynthesis and function of extracellular glycans in cyanobacteria
N2 - The cell surface of cyanobacteria is covered with glycans that confer versatility and adaptability to a multitude of environmental factors. The complex carbohydrates act as barriers against different types of stress and play a role in intra- as well as inter-species interactions. In this review, we summarize the current knowledge of the chemical composition, biosynthesis and biological function of exo- and lipo-polysaccharides from cyanobacteria and give an overview of sugar-binding lectins characterized from cyanobacteria. We discuss similarities with well-studied enterobacterial systems and highlight the unique features of cyanobacteria. We pay special attention to colony formation and EPS biosynthesis in the bloom-forming cyanobacterium, Microcystis aeruginosa.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 346
KW - cyanobacteria
KW - exopolysaccharides
KW - lipopolysaccharides
KW - colony formation
Y1 - 2017
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400121
ER -
TY - GEN
A1 - Elsner, Julia
A1 - Schibler, Jörg
A1 - Hofreiter, Michael
A1 - Schlumbaum, Angela
T1 - Burial condition is the most important factor for mtDNA PCR amplification success in Palaeolithic equid remains from the Alpine foreland
T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe
N2 - Faunal remains from Palaeolithic sites are important genetic sources to study preglacial and postglacial populations and to investigate the effect of climate change and human impact. Post mortem decay, resulting in fragmented and chemically modified DNA, is a key obstacle in ancient DNA analyses. In the absence of reliable methods to determine the presence of endogenous DNA in sub-fossil samples, temporal and spatial surveys of DNA survival on a regional scale may help to estimate the potential of faunal remains from a given time period and region. We therefore investigated PCR amplification success, PCR performance and post mortem damage in c. 47,000 to c. 12,000-year-old horse remains from 14 Palaeolithic sites along the Swiss Jura Mountains in relation to depositional context, tissue type, storage time and age, potentially influencing DNA preservation. The targeted 75 base pair mitochondrial DNA fragment could be amplified solely from equid remains from caves and not from any of the open dry and (temporary) wetland sites. Whether teeth are better than bones cannot be ultimately decided; however, both storage time after excavation and age significantly affect PCR amplification and performance, albeit not in a linear way. This is best explained by the—inevitable—heterogeneity of the data set. The extent of post mortem damage is not related to any of the potential impact factors. The results encourage comprehensive investigations of Palaeolithic cave sites, even from temperate regions.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 727
KW - ancient DNA
KW - DNA preservation
KW - horse
KW - cave
KW - Switzerland
Y1 - 2019
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-429763
SN - 1866-8372
IS - 727
SP - 505
EP - 515
ER -
TY - GEN
A1 - Jones, Eppie R.
A1 - González-Fortes, Gloria M.
A1 - Connell, Sarah
A1 - Siska, Veronika
A1 - Eriksson, Anders
A1 - Martiniano, Rui
A1 - McLaughlin, Russell L.
A1 - Llorente, Marcos Gallego
A1 - Cassidy, Lara M.
A1 - Gamba, Cristina
A1 - Meshveliani, Tengiz
A1 - Bar-Yosef, Ofer
A1 - Müller, Werner
A1 - Belfer-Cohen, Anna
A1 - Matskevich, Zinovi
A1 - Jakeli, Nino
A1 - Higham, Thomas F. G.
A1 - Currat, Mathias
A1 - Lordkipanidze, David
A1 - Hofreiter, Michael
A1 - Manica, Andrea
A1 - Pinhasi, Ron
A1 - Bradley, Daniel G.
T1 - Upper Palaeolithic genomes reveal deep roots of modern Eurasians
T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2 - We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ∼45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ∼25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ∼3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1334
Y1 - 2015
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-439317
SN - 1866-8372
IS - 1334
ER -
TY - GEN
A1 - Hartmann, Stefanie
A1 - Hasenkamp, Natascha
A1 - Mayer, Jens
A1 - Michaux, Johan
A1 - Morand, Serge
A1 - Mazzoni, Camila J.
A1 - Roca, Alfred L.
A1 - Greenwood, Alex D.
T1 - Endogenous murine leukemia retroviral variation across wild European and inbred strains of house mouse
T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2 - Background: Endogenous murine leukemia retroviruses (MLVs) are high copy number proviral elements difficult to comprehensively characterize using standard low throughput sequencing approaches. However, high throughput approaches generate data that is challenging to process, interpret and present.
Results: Next generation sequencing (NGS) data was generated for MLVs from two wild caught Mus musculus domesticus (from mainland France and Corsica) and for inbred laboratory mouse strains C3H, LP/J and SJL. Sequence reads were grouped using a novel sequence clustering approach as applied to retroviral sequences. A Markov cluster algorithm was employed, and the sequence reads were queried for matches to specific xenotropic (Xmv), polytropic (Pmv) and modified polytropic (Mpmv) viral reference sequences.
Conclusions: Various MLV subtypes were more widespread than expected among the mice, which may be due to the higher coverage of NGS, or to the presence of similar sequence across many different proviral loci. The results did not correlate with variation in the major MLV receptor Xpr1, which can restrict exogenous MLVs, suggesting that endogenous MLV distribution may reflect gene flow more than past resistance to infection.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1329
KW - murine leukemia virus
KW - endogenous retrovirus
KW - Xpr1
KW - XMRV
KW - genomic evolution
KW - Markov cluster algorithm
Y1 - 2015
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431200
SN - 1866-8372
IS - 1329
ER -
TY - GEN
A1 - Kappel, Christian
A1 - Trost, Gerda
A1 - Czesnick, Hjördis
A1 - Ramming, Anna
A1 - Kolbe, Benjamin
A1 - Vi, Song Lang
A1 - Bispo, Cláudia
A1 - Becker, Jörg D.
A1 - de Moor, Cornelia
A1 - Lenhard, Michael
T1 - Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana
N2 - The poly(A) tail at 3’ ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 259
KW - comprehensive analysis
KW - cytoplasmic polyadenylation
KW - differential expression analysis
KW - gene-expression
KW - mammalian-cells
KW - messenger-rna polyadenylation
KW - poly(a)-binding protein
KW - specificity factor
KW - tail-length
KW - translational control
Y1 - 2015
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-96400
SP - 1
EP - 30
ER -
TY - GEN
A1 - Sicard, Adrien
A1 - Kappel, Christian
A1 - Josephs, Emily B.
A1 - Wha Lee, Young
A1 - Marona, Cindy
A1 - Stinchcombe, John R.
A1 - Wright, Stephen I.
A1 - Lenhard, Michael
T1 - Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella
N2 - In the Bateson–Dobzhansky–Muller model of genetic incompatibilities post-zygotic gene-flow barriers arise by fixation of novel alleles at interacting loci in separated populations. Many such incompatibilities are polymorphic in plants, implying an important role for genetic drift or balancing selection in their origin and evolution. Here we show that NPR1 and RPP5 loci cause a genetic incompatibility between the incipient species Capsella grandiflora and C. rubella, and the more distantly related C. rubella and C. orientalis. The incompatible RPP5 allele results from a mutation in C. rubella, while the incompatible NPR1 allele is frequent in the ancestral C. grandiflora. Compatible and incompatible NPR1 haplotypes are maintained by balancing selection in C. grandiflora, and were divergently sorted into the derived C. rubella and C. orientalis. Thus, by maintaining differentiated alleles at high frequencies, balancing selection on ancestral polymorphisms can facilitate establishing gene-flow barriers between derived populations through lineage sorting of the alternative alleles.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 231
Y1 - 2015
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-93568
ER -
TY - GEN
A1 - Üstün, Suayib
A1 - Bartetzko, Verena
A1 - Börnke, Frederik
T1 - The Xanthomonas effector XopJ triggers a conditional hypersensitive response upon treatment of N. benthamiana leaves with salicylic acid
T2 - Frontiers in plant science
N2 - XopJ is a Xanthomonas type III effector protein that promotes bacterial virulence on susceptible pepper plants through the inhibition of the host cell proteasome and a resultant suppression of salicylic acid (SA) - dependent defense responses. We show here that Nicotiana benthamiana leaves transiently expressing XopJ display hypersensitive response (HR) -like symptoms when exogenously treated with SA. This apparent avirulence function of XopJ was further dependent on effector myristoylation as well as on an intact catalytic triad, suggesting a requirement of its enzymatic activity for HR-like symptom elicitation. The ability of XopJ to cause a HR-like symptom development upon SA treatment was lost upon silencing of SGT1 and NDR1, respectively, but was independent of EDS1 silencing, suggesting that XopJ is recognized by an R protein of the CC-NBS-LRR class. Furthermore, silencing of NPR1 abolished the elicitation of HR-like symptoms in XopJ expressing leaves after SA application. Measurement of the proteasome activity indicated that proteasome inhibition by XopJ was alleviated in the presence of SA, an effect that was not observed in NPR1 silenced plants. Our results suggest that XopJ - triggered HR-like symptoms are closely related to the virulence function of the effector and that XopJ follows a two-signal model in order to elicit a response in the non-host plant N. benthamiana.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 432
KW - Xanthomonas
KW - type-III effector
KW - XopJ
KW - avirulence
KW - salicylic acid
Y1 - 2018
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-406537
ER -
TY - GEN
A1 - Klauschies, Toni
A1 - Vasseur, David A.
A1 - Gaedke, Ursula
T1 - Trait adaptation promotes species coexistence in diverse predator and prey communities
N2 - Species can adjust their traits in response to selection which may strongly influence species coexistence. Nevertheless, current theory mainly assumes distinct and time-invariant trait values. We examined the combined effects of the range and the speed of trait adaptation on species coexistence using an innovative multispecies predator–prey model. It allows for temporal trait changes of all predator and prey species and thus simultaneous coadaptation within and among trophic levels. We show that very small or slow trait adaptation did not facilitate coexistence because the stabilizing niche differences were not sufficient to offset the fitness differences. In contrast, sufficiently large and fast trait adaptation jointly promoted stable or neutrally stable species coexistence. Continuous trait adjustments in response to selection enabled a temporally variable convergence and divergence of species traits; that is, species became temporally more similar (neutral theory) or dissimilar (niche theory) depending on the selection pressure, resulting over time in a balance between niche differences stabilizing coexistence and fitness differences promoting competitive exclusion. Furthermore, coadaptation allowed prey and predator species to cluster into different functional groups. This equalized the fitness of similar species while maintaining sufficient niche differences among functionally different species delaying or preventing competitive exclusion. In contrast to previous studies, the emergent feedback between biomass and trait dynamics enabled supersaturated coexistence for a broad range of potential trait adaptation and parameters. We conclude that accounting for trait adaptation may explain stable and supersaturated species coexistence for a broad range of environmental conditions in natural systems when the absence of such adaptive changes would preclude it. Small trait changes, coincident with those that may occur within many natural populations, greatly enlarged the number of coexisting species.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 227
KW - Coadaptation
KW - equalizing and stabilizing mechanisms
KW - maintenance of functional diversity
KW - niche and fitness differences
KW - supersaturated species coexistence
KW - trait convergence and divergence
Y1 - 2016
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-91498
SN - 1866-8372
ER -
TY - GEN
A1 - Lah, Ljerka
A1 - Trense, Daronja
A1 - Benke, Harald
A1 - Berggren, Per
A1 - Gunnlaugsson, Þorvaldur
A1 - Lockyer, Christina
A1 - Öztürk, Ayaka
A1 - Öztürk, Bayram
A1 - Pawliczka, Iwona
A1 - Roos, Anna
A1 - Siebert, Ursula
A1 - Skóra, Krzysztof
A1 - Víkingsson, Gísli
A1 - Tiedemann, Ralph
T1 - Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise
N2 - The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-by-distance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, using a population genomics approach. We used 2872 single nucleotide polymorphisms (SNPs), derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), as well as 13 microsatellite loci and mitochondrial haplotypes for the same set of individuals. Spatial principal components analysis (sPCA), and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 295
Y1 - 2016
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-100813
SN - 1866-8372
ER -
TY - GEN
A1 - Zhu, Fangjun
A1 - Schlupp, Ingo
A1 - Tiedemann, Ralph
T1 - Sequence Evolution and Expression of the Androgen Receptor and Other Pathway-Related Genes in a Unisexual Fish, the Amazon Molly, Poecilia formosa, and Its Bisexual Ancestors
N2 - The all-female Amazon molly (Poecilia formosa) originated from a single hybridization of two bisexual ancestors, Atlantic molly (Poecilia mexicana) and sailfin molly (Poecilia latipinna). As a gynogenetic species, the Amazon molly needs to copulate with a heterospecific male, but the genetic information of the sperm-donor does not contribute to the next generation, as the sperm only acts as the trigger for the diploid eggs’ embryogenesis. Here, we study the sequence evolution and gene expression of the duplicated genes coding for androgen receptors (ars) and other pathway-related genes, i.e., the estrogen receptors (ers) and cytochrome P450, family19, subfamily A, aromatase genes (cyp19as), in the Amazon molly, in comparison to its bisexual ancestors. Mollies possess–as most other teleost fish—two copies of the ar, er, and cyp19a genes, i.e., arα/arβ, erα/erβ1, and cyp19a1 (also referred as cyp19a1a)/cyp19a2 (also referred to as cyp19a1b), respectively. Non-synonymous single nucleotide polymorphisms (SNPs) among the ancestral bisexual species were generally predicted not to alter protein function. Some derived substitutions in the P. mexicana and one in P. formosa are predicted to impact protein function. We also describe the gene expression pattern of the ars and pathway-related genes in various tissues (i.e., brain, gill, and ovary) and provide SNP markers for allele specific expression research. As a general tendency, the levels of gene expression were lowest in gill and highest in ovarian tissues, while expression levels in the brain were intermediate in most cases. Expression levels in P. formosa were conserved where expression did not differ between the two bisexual ancestors. In those cases where gene expression levels significantly differed between the bisexual species, P. formosa expression was always comparable to the higher expression level among the two ancestors. Interestingly, erβ1 was expressed neither in brain nor in gill in the analyzed three molly species, which implies a more important role of erα in the estradiol synthesis pathway in these tissues. Furthermore, our data suggest that interactions of steroid-signaling pathway genes differ across tissues, in particular the interactions of ars and cyp19as.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 265
Y1 - 2016
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-97119
ER -
TY - GEN
A1 - Batsios, Petros
A1 - Ren, Xiang
A1 - Baumann, Otto
A1 - Larochelle, Denis A.
A1 - Gräf, Ralph
T1 - Src1 is a Protein of the Inner Nuclear Membrane Interacting with the Dictyostelium Lamin NE81
N2 - The nuclear envelope (NE) consists of the outer and inner nuclear membrane (INM), whereby the latter is bound to the nuclear lamina. Src1 is a Dictyostelium homologue of the helix-extension-helix family of proteins, which also includes the human lamin-binding protein MAN1. Both endogenous Src1 and GFP-Src1 are localized to the NE during the entire cell cycle. Immuno-electron microscopy and light microscopy after differential detergent treatment indicated that Src1 resides in the INM. FRAP experiments with GFP-Src1 cells suggested that at least a fraction of the protein could be stably engaged in forming the nuclear lamina together with the Dictyostelium lamin NE81. Both a BioID proximity assay and mis-localization of soluble, truncated mRFP-Src1 at cytosolic clusters consisting of an intentionally mis-localized mutant of GFP-NE81 confirmed an interaction of Src1 and NE81. Expression GFP-Src11–646, a fragment C-terminally truncated after the first transmembrane domain, disrupted interaction of nuclear membranes with the nuclear lamina, as cells formed protrusions of the NE that were dependent on cytoskeletal pulling forces. Protrusions were dependent on intact microtubules but not actin filaments. Our results indicate that Src1 is required for integrity of the NE and highlight Dictyostelium as a promising model for the evolution of nuclear architecture.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 263
KW - Dictyostelium
KW - HeH-protein
KW - LEM-domain protein
KW - lamin
KW - nuclear lamina
KW - nucleolus
KW - nucleus
Y1 - 2016
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-97033
ER -
TY - GEN
A1 - Rainford, James L.
A1 - Hofreiter, Michael
A1 - Mayhew, Peter J.
T1 - Phylogenetic analyses suggest that diversification and body size evolution are independent in insects
T2 - BMC evolutionary biology
N2 - Background:
Skewed body size distributions and the high relative richness of small-bodied taxa are a fundamental
property of a wide range of animal clades. The evolutionary processes responsible for generating these distributions
are well described in vertebrate model systems but have yet to be explored in detail for other major terrestrial
clades. In this study, we explore the macro-evolutionary patterns of body size variation across families of Hexapoda
(insects and their close relatives), using recent advances in phylogenetic understanding, with an aim to investigate
the link between size and diversity within this ancient and highly diverse lineage.
Results:
The maximum, minimum and mean-log body lengths of hexapod families are all approximately log-normally
distributed, consistent with previous studies at lower taxonomic levels, and contrasting with skewed distributions
typical of vertebrate groups. After taking phylogeny and within-tip variation into account, we find no evidence for a
negative relationship between diversification rate and body size, suggesting decoupling of the forces controlling these
two traits. Likelihood-based modeling of the log-mean body size identifies distinct processes operating within
Holometabola and Diptera compared with other hexapod groups, consistent with accelerating rates of size evolution
within these clades, while as a whole, hexapod body size evolution is found to be dominated by neutral processes
including significant phylogenetic conservatism.
Conclusions:
Based on our findings we suggest that the use of models derived from well-studied but atypical clades,
such as vertebrates may lead to misleading conclusions when applied to other major terrestrial lineages. Our results
indicate that within hexapods, and within the limits of current systematic and phylogenetic knowledge, insect
diversification is generally unfettered by size-biased macro-evolutionary processes, and that these processes over large
timescales tend to converge on apparently neutral evolutionary processes. We also identify limitations on available
data within the clade and modeling approaches for the resolution of trees of higher taxa, the resolution of which may
collectively enhance our understanding of this key component of terrestrial ecosystems.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 441
KW - body size
KW - diversification
KW - hexapoda
KW - insects
KW - phylogeny
Y1 - 2018
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407328
ER -
TY - GEN
A1 - Liaimer, Anton
A1 - Jensen, John B.
A1 - Dittmann-Thünemann, Elke
T1 - A genetic and chemical perspective on symbiotic recruitment of cyanobacteria of the genus Nostoc into the host plant Blasia pusilla L.
T2 - Frontiers in microbiology
N2 - Liverwort Blasia pusilla L. recruits soil nitrogen-fixing cyanobacteria of genus Nostoc as symbiotic partners. In this work we compared Nostoc community composition inside the plants and in the soil around them from two distant locations in Northern Norway. STRR fingerprinting and 16S rDNA phylogeny reconstruction showed a remarkable local diversity among isolates assigned to several Nostoc clades. An extensive web of negative allelopathic interactions was recorded at an agricultural site, but not at the undisturbed natural site. The cell extracts of the cyanobacteria did not show antimicrobial activities, but four isolates were shown to be cytotoxic to human cells. The secondary metabolite profiles of the isolates were mapped by MALDI-TOF MS, and the most prominent ions were further analyzed by Q-TOF for MS/MS aided identification. Symbiotic isolates produced a great variety of small peptide-like substances, most of which lack any record in the databases. Among identified compounds we found microcystin and nodularin variants toxic to eukaryotic cells. Microcystin producing chemotypes were dominating as symbiotic recruits but not in the free-living community. In addition, we were able to identify several novel aeruginosins and banyaside-like compounds, as well as nostocyclopeptides and nosperin.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 434
KW - cyanobacteria
KW - secondary metabolites
KW - symbiosis
KW - Blasia
KW - Nostoc
KW - allelopathy
Y1 - 2018
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407179
ER -
TY - GEN
A1 - Krupinski, Pawel
A1 - Bozorg, Behruz
A1 - Larsson, André
A1 - Pietra, Stefano
A1 - Grebe, Markus
A1 - Jönsson, Henrik
T1 - A model analysis of mechanisms for radial microtubular patterns at root hair initiation sites
T2 - Frontiers in plant science
N2 - Plant cells have two main modes of growth generating anisotropic structures. Diffuse growth where whole cell walls extend in specific directions, guided by anisotropically positioned cellulose fibers, and tip growth, with inhomogeneous addition of new cell wall material at the tip of the structure. Cells are known to regulate these processes via molecular signals and the cytoskeleton. Mechanical stress has been proposed to provide an input to the positioning of the cellulose fibers via cortical microtubules in diffuse growth. In particular, a stress feedback model predicts a circumferential pattern of fibers surrounding apical tissues and growing primordia, guided by the anisotropic curvature in such tissues. In contrast, during the initiation of tip growing root hairs, a star-like radial pattern has recently been observed. Here, we use detailed finite element models to analyze how a change in mechanical properties at the root hair initiation site can lead to star-like stress patterns in order to understand whether a stress-based feedback model can also explain the microtubule patterns seen during root hair initiation. We show that two independent mechanisms, individually or combined, can be sufficient to generate radial patterns. In the first, new material is added locally at the position of the root hair. In the second, increased tension in the initiation area provides a mechanism. Finally, we describe how a molecular model of Rho-of-plant (ROP) GTPases activation driven by auxin can position a patch of activated ROP protein basally along a 2D root epidermal cell plasma membrane, paving the way for models where mechanical and molecular mechanisms cooperate in the initial placement and outgrowth of root hairs.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 435
KW - plant cell wall
KW - finite element modeling
KW - computational morphodynamics
KW - root hair initiation
KW - microtubules
KW - cellulose fibers
KW - composite material
Y1 - 2018
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407181
ER -
TY - GEN
A1 - Lukoszek, Radoslaw
A1 - Feist, Peter
A1 - Ignatova, Zoya
T1 - Insights into the adaptive response of Arabidopsis thaliana to prolonged thermal stress by ribosomal profiling and RNA-Seq
T2 - BMC plant biology
N2 - Background:
Environmental stress puts organisms at risk and requires specific stress-tailored responses to maximize
survival. Long-term exposure to stress necessitates a global reprogramming of the cellular activities at different
levels of gene expression.
Results:
Here, we use ribosome profiling and RNA sequencing to globally profile the adaptive response of
Arabidopsis thaliana
to prolonged heat stress. To adapt to long heat exposure, the expression of many genes is
modulated in a coordinated manner at a transcriptional and translational level. However, a significant group of
genes opposes this trend and shows mainly translational regulation. Different secondary structure elements are
likely candidates to play a role in regulating translation of those genes.
Conclusions:
Our data also uncover on how the subunit stoichiometry of multimeric protein complexes in plastids
is maintained upon heat exposure.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 438
KW - translation
KW - ribosome profiling
KW - transcription
KW - RNA-Seq
KW - secondary structure
KW - G-quadruplexes,
KW - heat stress response
Y1 - 2018
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407262
ER -
TY - GEN
A1 - Navarro-Retamal, Carlos
A1 - Bremer, Anne
A1 - Alzate-Morales, Jans H.
A1 - Caballero, Julio
A1 - Hincha, Dirk K.
A1 - González, Wendy
A1 - Thalhammer, Anja
T1 - Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana
N2 - The LEA (late embryogenesis abundant) proteins COR15A and COR15B from Arabidopsis thaliana are intrinsically disordered under fully hydrated conditions, but obtain α-helical structure during dehydration, which is reversible upon rehydration. To understand this unusual structural transition, both proteins were investigated by circular dichroism (CD) and molecular dynamics (MD) approaches. MD simulations showed unfolding of the proteins in water, in agreement with CD data obtained with both HIS-tagged and untagged recombinant proteins. Mainly intramolecular hydrogen bonds (H-bonds) formed by the protein backbone were replaced by H-bonds with water molecules. As COR15 proteins function in vivo as protectants in leaves partially dehydrated by freezing, unfolding was further assessed under crowded conditions. Glycerol reduced (40%) or prevented (100%) unfolding during MD simulations, in agreement with CD spectroscopy results. H-bonding analysis indicated that preferential exclusion of glycerol from the protein backbone increased stability of the folded state.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 321
Y1 - 2016
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-394503
SP - 25806
EP - 25816
ER -
TY - GEN
A1 - Wacker, Alexander
A1 - Piepho, Maike
A1 - Harwood, John L.
A1 - Guschina, Irina A.
A1 - Arts, Michael T.
T1 - Light-Induced Changes in Fatty Acid Profiles of Specific Lipid Classes in Several Freshwater Phytoplankton Species
N2 - We tested the influence of two light intensities [40 and 300 μmol PAR / (m2s)] on the fatty acid composition of three distinct lipid classes in four freshwater phytoplankton species. We chose species of different taxonomic classes in order to detect potentially similar reaction characteristics that might also be present in natural phytoplankton communities. From samples of the bacillariophyte Asterionella formosa, the chrysophyte Chromulina sp., the cryptophyte Cryptomonas ovata and the zygnematophyte Cosmarium botrytis we first separated glycolipids (monogalactosyldiacylglycerol, digalactosyldiacylglycerol, and sulfoquinovosyldiacylglycerol), phospholipids (phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, and phosphatidylserine) as well as non-polar lipids (triacylglycerols), before analyzing the fatty acid composition of each lipid class. High variation in the fatty acid composition existed among different species. Individual fatty acid compositions differed in their reaction to changing light intensities in the four species. Although no generalizations could be made for species across taxonomic classes, individual species showed clear but small responses in their ecologically-relevant omega-3 and omega-6 polyunsaturated fatty acids (PUFA) in terms of proportions and of per tissue carbon quotas. Knowledge on how lipids like fatty acids change with environmental or culture conditions is of great interest in ecological food web studies, aquaculture, and biotechnology, since algal lipids are the most important sources of omega-3 long-chain PUFA for aquatic and terrestrial consumers, including humans.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 223
KW - fatty acid changes
KW - freshwater algae
KW - light adaptation
KW - lipid classes
Y1 - 2016
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-90682
SP - 1
EP - 13
ER -
TY - GEN
A1 - Zancolli, Giulia
A1 - Baker, Timothy G.
A1 - Barlow, Axel
A1 - Bradley, Rebecca K.
A1 - Calvete, Juan J.
A1 - Carter, Kimberley C.
A1 - de Jager, Kaylah
A1 - Owens, John Benjamin
A1 - Price, Jenny Forrester
A1 - Sanz, Libia
A1 - Scholes-Higham, Amy
A1 - Shier, Liam
A1 - Wood, Liam
A1 - Wüster, Catharine E.
A1 - Wüster, Wolfgang
T1 - Is hybridization a source of adaptive venom variation in rattlesnakes?
BT - a test, using a crotalus scutulatus × viridis hybrid zone in southwestern New Mexico
T2 - Toxins
N2 - Venomous snakes often display extensive variation in venom composition both between and within species. However, the mechanisms underlying the distribution of different toxins and venom types among populations and taxa remain insufficiently known. Rattlesnakes (Crotalus, Sistrurus) display extreme inter-and intraspecific variation in venom composition, centered particularly on the presence or absence of presynaptically neurotoxic phospholipases A2 such as Mojave toxin (MTX). Interspecific hybridization has been invoked as a mechanism to explain the distribution of these toxins across rattlesnakes, with the implicit assumption that they are adaptively advantageous. Here, we test the potential of adaptive hybridization as a mechanism for venom evolution by assessing the distribution of genes encoding the acidic and basic subunits of Mojave toxin across a hybrid zone between MTX-positive Crotalus scutulatus and MTX-negative C. viridis in southwestern New Mexico, USA. Analyses of morphology, mitochondrial and single copy-nuclear genes document extensive admixture within a narrow hybrid zone. The genes encoding the two MTX subunits are strictly linked, and found in most hybrids and backcrossed individuals, but not in C. viridis away from the hybrid zone. Presence of the genes is invariably associated with presence of the corresponding toxin in the venom. We conclude that introgression of highly lethal neurotoxins through hybridization is not necessarily favored by natural selection in rattlesnakes, and that even extensive hybridization may not lead to introgression of these genes into another species.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 443
KW - adaptation
KW - Crotalus
KW - evolution
KW - hybridization
KW - introgression
KW - Mojave toxin
KW - molecular evolution
KW - venom
Y1 - 2018
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407595
ER -
TY - GEN
A1 - Wessig, Pablo
A1 - Bader, Denise
A1 - Klier, Dennis Tobias
A1 - Hettrich, Cornelia
A1 - Bier, Frank Fabian
T1 - Detecting carbohydrate–lectin interactions using a fluorescent probe based on DBD dyes
N2 - Herein we present an efficient synthesis of a biomimetic probe with modular construction that can be specifically bound by the mannose binding FimH protein – a surface adhesion protein of E. coli bacteria. The synthesis combines the new and interesting DBD dye with the carbohydrate ligand mannose via a Click reaction. We demonstrate the binding to E. coli bacteria over a large concentration range and also present some special characteristics of those molecules that are of particular interest for the application as a biosensor. In particular, the mix-and-measure ability and the very good photo-stability should be highlighted here.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 314
KW - conformational-changes
KW - green-i
KW - protein
KW - binding
KW - assay
Y1 - 2016
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-394382
SP - 1235
EP - 1238
ER -
TY - GEN
A1 - Roggenbuck, Dirk
A1 - Borghi, Maria Orietta
A1 - Somma, Valentina
A1 - Büttner, Thomas
A1 - Schierack, Peter
A1 - Hanack, Katja
A1 - Grossi, Claudia
A1 - Bodio, Caterina
A1 - Macor, Paolo
A1 - von Landenberg, Philipp
A1 - Boccellato, Francesco
A1 - Mahler, Michael
A1 - Meroni, Pier Luigi
T1 - Antiphospholipid antibodies detected by line immunoassay differentiate among patients with antiphospholipid syndrome, with infections and asymptomatic carriers
T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe
N2 - Background
Antiphospholipid antibodies (aPL) can be detected in asymptomatic carriers and infectious patients. The aim was to investigate whether a novel line immunoassay (LIA) differentiates between antiphospholipid syndrome (APS) and asymptomatic aPL+ carriers or patients with infectious diseases (infectious diseases controls (IDC)).
Methods
Sixty-one patients with APS (56 primary, 22/56 with obstetric events only, and 5 secondary), 146 controls including 24 aPL+ asymptomatic carriers and 73 IDC were tested on a novel hydrophobic solid phase coated with cardiolipin (CL), phosphatic acid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylserine, beta2-glycoprotein I (β2GPI), prothrombin, and annexin V. Samples were also tested by anti-CL and anti-β2GPI ELISAs and for lupus anticoagulant activity. Human monoclonal antibodies (humoAbs) against human β2GPI or PL alone were tested on the same LIA substrates in the absence or presence of human serum, purified human β2GPI or after CL-micelle absorption.
Results
Comparison of LIA with the aPL-classification assays revealed good agreement for IgG/IgM aß2GPI and aCL. Anti-CL and anti-ß2GPI IgG/IgM reactivity assessed by LIA was significantly higher in patients with APS versus healthy controls and IDCs, as detected by ELISA. IgG binding to CL and ß2GPI in the LIA was significantly lower in aPL+ carriers and Venereal Disease Research Laboratory test (VDRL) + samples than in patients with APS. HumoAb against domain 1 recognized β2GPI bound to the LIA-matrix and in anionic phospholipid (PL) complexes. Absorption with CL micelles abolished the reactivity of a PL-specific humoAb but did not affect the binding of anti-β2GPI humoAbs.
Conclusions
The LIA and ELISA have good agreement in detecting aPL in APS, but the LIA differentiates patients with APS from infectious patients and asymptomatic carriers, likely through the exposure of domain 1.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 436
KW - Antiphospholipid syndrome
KW - Antiphospholipid antibody
KW - Phospholipid binding proteins
KW - Beta2 - glycoprotein I
KW - Line immunoassay
Y1 - 2018
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407211
SN - 1866-8372
IS - 436
ER -
TY - GEN
A1 - Ćwiek-Kupczyńska, Hanna
A1 - Altmann, Thomas
A1 - Arend, Daniel
A1 - Arnaud, Elizabeth
A1 - Chen, Dijun
A1 - Cornut, Guillaume
A1 - Fiorani, Fabio
A1 - Frohmberg, Wojciech
A1 - Junker, Astrid
A1 - Klukas, Christian
A1 - Lange, Matthias
A1 - Mazurek, Cezary
A1 - Nafissi, Anahita
A1 - Neveu, Pascal
A1 - van Oeveren, Jan
A1 - Pommier, Cyril
A1 - Poorter, Hendrik
A1 - Rocca-Serra, Philippe
A1 - Sansone, Susanna-Assunta
A1 - Scholz, Uwe
A1 - van Schriek, Marco
A1 - Seren, Ümit
A1 - Usadel, Björn
A1 - Weise, Stephan
A1 - Kersey, Paul
A1 - Krajewski, Paweł
T1 - Measures for interoperability of phenotypic data
BT - minimum information requirements and formatting
T2 - Plant methods
N2 - Background:
Plant phenotypic data shrouds a wealth of information which, when accurately analysed and linked
to other data types, brings to light the knowledge about the mechanisms of life. As phenotyping is a field of research
comprising manifold, diverse and time
‑consuming experiments, the findings can be fostered by reusing and combin‑
ing existing datasets. Their correct interpretation, and thus replicability, comparability and interoperability, is possible
provided that the collected observations are equipped with an adequate set of metadata. So far there have been no
common standards governing phenotypic data description, which hampered data exchange and reuse.
Results:
In this paper we propose the guidelines for proper handling of the information about plant phenotyping
experiments, in terms of both the recommended content of the description and its formatting. We provide a docu‑
ment called “Minimum Information About a Plant Phenotyping Experiment”, which specifies what information about
each experiment should be given, and a Phenotyping Configuration for the ISA
‑Tab format, which allows to practically
organise this information within a dataset. We provide examples of ISA
‑Tab
‑formatted phenotypic data, and a general
description of a few systems where the recommendations have been implemented.
Conclusions:
Acceptance of the rules described in this paper by the plant phenotyping community will help to
achieve findable, accessible, interoperable and reusable data.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 450
KW - data standardisation and formatting
KW - experimental metadata
KW - minimum information recommendations
KW - plant phenotyping
KW - experiment description
Y1 - 2018
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407299
ER -