TY  - JOUR
A1  - Fritz, Michael Andre
A1  - Rosa, Stefanie
A1  - Sicard, Adrien
T1  - Mechanisms Underlying the Environmentally Induced Plasticity of Leaf Morphology
JF  - Frontiers in genetics
N2  - The primary function of leaves is to provide an interface between plants and their environment for gas exchange, light exposure and thermoregulation. Leaves have, therefore a central contribution to plant fitness by allowing an efficient absorption of sunlight energy through photosynthesis to ensure an optimal growth. Their final geometry will result from a balance between the need to maximize energy uptake while minimizing the damage caused by environmental stresses. This intimate relationship between leaf and its surroundings has led to an enormous diversification in leaf forms. Leaf shape varies between species, populations, individuals or even within identical genotypes when those are subjected to different environmental conditions. For instance, the extent of leaf margin dissection has, for long, been found to inversely correlate with the mean annual temperature, such that Paleobotanists have used models based on leaf shape to predict the paleoclimate from fossil flora. Leaf growth is not only dependent on temperature but is also regulated by many other environmental factors such as light quality and intensity or ambient humidity. This raises the question of how the different signals can be integrated at the molecular level and converted into clear developmental decisions. Several recent studies have started to shed the light on the molecular mechanisms that connect the environmental sensing with organ-growth and patterning. In this review, we discuss the current knowledge on the influence of different environmental signals on leaf size and shape, their integration as well as their importance for plant adaptation.
KW  - plants
KW  - leaf morphology
KW  - environment
KW  - developmental plasticity
KW  - gene regulatory networks
KW  - sensory system
KW  - gene responsiveness
Y1  - 2018
U6  - https://doi.org/10.3389/fgene.2018.00478
SN  - 1664-8021
VL  - 9
PB  - Frontiers Research Foundation
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Ambarli, Hüseyin
A1  - Mengüllüoğlu, Deniz
A1  - Fickel, Jörns
A1  - Förster, Daniel W.
T1  - Hotel AMANO Grand Central of brown bears in southwest Asia
JF  - PeerJ
N2  - Genetic studies of the Eurasian brown bear (Ursus arctos) have so far focused on populations from Europe and North America, although the largest distribution area of brown bears is in Asia. In this study, we reveal population genetic parameters for the brown bear population inhabiting the Grand Kackar Mountains (GKM) in the north east of Turkey, western Lesser Caucasus. Using both hair (N = 147) and tissue samples (N = 7) collected between 2008 and 2014, we found substantial levels of genetic variation (10 microsatellite loci). Bear samples (hair) taken from rubbing trees worked better for genotyping than those from power poles, regardless of the year collected. Genotyping also revealed that bears moved between habitat patches, despite ongoing massive habitat alterations and the creation of large water reservoirs. This population has the potential to serve as a genetic reserve for future reintroduction in the Middle East. Due to the importance of the GKM population for on-going and future conservation actions, the impacts of habitat alterations in the region ought to be minimized; e.g., by establishing green bridges or corridors over reservoirs and major roads to maintain habitat connectivity and gene flow among populations in the Lesser Caucasus.
KW  - Ursus arctos
KW  - Microsatellite
KW  - Conservation
KW  - Anatolia
KW  - Isolation
KW  - Source population
KW  - Noninvasive sampling
KW  - Rubbing tree
KW  - Turkey
Y1  - 2018
U6  - https://doi.org/10.7717/peerj.5660
SN  - 2167-8359
VL  - 6
PB  - PeerJ Inc.
CY  - London
ER  - 
TY  - JOUR
A1  - Mengüllüoğlu, Deniz
A1  - Fickel, Jörns
A1  - Hofer, Heribert
A1  - Förster, Daniel W.
T1  - Non-invasive faecal sampling reveals spatial organization and improves measures of genetic diversity for the conservation assessment of territorial species
BT  - Caucasian lynx as a case species
JF  - PLoS one
N2  - The Caucasian lynx, Lynx lynx dinniki, has one of the southernmost distributions in the Eurasian lynx range, covering Anatolian Turkey, the Caucasus and Iran. Little is known about the biology and the genetic status of this subspecies. To collect baseline genetic, ecological and behavioural data and benefit future conservation of L. l. dinniki, we monitored 11 lynx territories (396 km(2)) in northwestern Anatolia. We assessed genetic diversity of this population by non-invasively collecting 171 faecal samples and trapped and sampled 12 lynx individuals using box traps. We observed high allelic variation at 11 nuclear microsatellite markers, and found no signs of inbreeding despite the potential isolation of this population. We obtained similar numbers of distinct genotypes from the two sampling sources. Our results indicated that first order female relatives occupy neighbouring territories (female philopatry) and that territorial male lynx were highly unrelated to each other and to female territorial lynx, suggesting long distance male dispersal. Particular male and female resident territorial lynx and their offspring (kittens and subadults) were more likely to be trapped than resident floaters or dispersing (unrelated) lynx. Conversely, we obtained more data for unrelated lynx and higher numbers of territorials using non-invasive sampling (faeces). When invasive and non-invasive samples were analysed separately, the spatial organisation of lynx (in terms of female philopatry and females and males occupying permanent ranges) affected measures of genetic diversity in such a way that estimates of genetic diversity were reduced if only invasive samples were considered. It appears that, at small spatial scales, invasive sampling using box traps may underestimate the genetic diversity in carnivores with permanent ranges and philopatry such as the Eurasian lynx. As non-invasive sampling can also provide additional data on diet and spatial organisation, we advocate the use of such samples for conservation genetic studies of vulnerable, endangered or data deficient territorial species.
Y1  - 2019
U6  - https://doi.org/10.1371/journal.pone.0216549
SN  - 1932-6203
VL  - 14
IS  - 5
PB  - PLoS
CY  - San Fransisco
ER  - 
TY  - JOUR
A1  - Berry, Scott
A1  - Rosa, Stefanie
A1  - Howard, Martin
A1  - Buhler, Marc
A1  - Dean, Caroline
T1  - Disruption of an RNA-binding hinge region abolishes LHP1-mediated epigenetic repression
JF  - Genes & Development
N2  - Epigenetic maintenance of gene repression is essential for development. Polycomb complexes are central to this memory, but many aspects of the underlying mechanism remain unclear. LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) binds Polycomb-deposited H3K27me3 and is required for repression of many Polycomb target genes in Arabidopsis. Here we show that LHP1 binds RNA in vitro through the intrinsically disordered hinge region. By independently perturbing the RNA-binding hinge region and H3K27me3 (trimethylation of histone H3 at Lys27) recognition, we found that both facilitate LHP1 localization and H3K27me3 maintenance. Disruption of the RNAbinding hinge region also prevented formation of subnuclear foci, structures potentially important for epigenetic repression.
KW  - chromatin
KW  - epigenetics
KW  - plant biology
KW  - Polycomb
KW  - RNA
Y1  - 2017
U6  - https://doi.org/10.1101/gad.305227.117
SN  - 0890-9369
SN  - 1549-5477
VL  - 31
SP  - 2115
EP  - 2120
PB  - Cold Spring Harbor Laboratory Press
CY  - Cold Spring Harbor, NY
ER  - 
TY  - JOUR
A1  - Wendler, Petra
A1  - Enenkel, Cordula
T1  - Nuclear Transport of Yeast Proteasomes
JF  - Frontiers in molecular biosciences
N2  - Proteasomes are key proteases in regulating protein homeostasis. Their holo-enzymes are composed of 40 different subunits which are arranged in a proteolytic core (CP) flanked by one to two regulatory particles (RP). Proteasomal proteolysis is essential for the degradation of proteins which control time-sensitive processes like cell cycle progression and stress response. In dividing yeast and human cells, proteasomes are primarily nuclear suggesting that proteasomal proteolysis is mainly required in the nucleus during cell proliferation. In yeast, which have a closed mitosis, proteasomes are imported into the nucleus as immature precursors via the classical import pathway. During quiescence, the reversible absence of proliferation induced by nutrient depletion or growth factor deprivation, proteasomes move from the nucleus into the cytoplasm. In the cytoplasm of quiescent yeast, proteasomes are dissociated into CP and RP and stored in membrane-less cytoplasmic foci, named proteasome storage granules (PSGs). With the resumption of growth, PSGs clear and mature proteasomes are transported into the nucleus by Blm10, a conserved 240 kDa protein and proteasome-intrinsic import receptor. How proteasomes are exported from the nucleus into the cytoplasm is unknown.
KW  - proteasome
KW  - nuclear transport
KW  - importin
KW  - karyopherin
KW  - Blm10
KW  - proteasome storage granules
Y1  - 2019
U6  - https://doi.org/10.3389/fmolb.2019.00034
SN  - 2296-889X
VL  - 6
PB  - Frontiers Research Foundation
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Möser, Christin
A1  - Lorenz, Jessica S.
A1  - Sajfutdinow, Martin
A1  - Smith, David M.
T1  - Pinpointed Stimulation of EphA2 Receptors via DNA-Templated Oligovalence
JF  - International journal of molecular sciences
N2  - DNA nanostructures enable the attachment of functional molecules to nearly any unique location on their underlying structure. Due to their single-base-pair structural resolution, several ligands can be spatially arranged and closely controlled according to the geometry of their desired target, resulting in optimized binding and/or signaling interactions. Here, the efficacy of SWL, an ephrin-mimicking peptide that binds specifically to EphrinA2 (EphA2) receptors, increased by presenting up to three of these peptides on small DNA nanostructures in an oligovalent manner. Ephrin signaling pathways play crucial roles in tumor development and progression. Moreover, Eph receptors are potential targets in cancer diagnosis and treatment. Here, the quantitative impact of SWL valency on binding, phosphorylation (key player for activation) and phenotype regulation in EphA2-expressing prostate cancer cells was demonstrated. EphA2 phosphorylation was significantly increased by DNA trimers carrying three SWL peptides compared to monovalent SWL. In comparison to one of EphA2’s natural ligands ephrin-A1, which is known to bind promiscuously to multiple receptors, pinpointed targeting of EphA2 by oligovalent DNA-SWL constructs showed enhanced cell retraction. Overall, we show that DNA scaffolds can increase the potency of weak signaling peptides through oligovalent presentation and serve as potential tools for examination of complex signaling pathways.
KW  - DNA nanostructure
KW  - ephrin
KW  - EphA2
KW  - SWL
KW  - PC-3 cells
KW  - multivalence
Y1  - 2018
U6  - https://doi.org/10.3390/ijms19113482
SN  - 1422-0067
VL  - 19
IS  - 11
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Schwanhold, Nadine
A1  - Iobbi-Nivol, Chantal
A1  - Lehmann, Angelika
A1  - Leimkühler, Silke
T1  - Same but different
BT  - Comparison of two system-specific molecular chaperones for the maturation of formate dehydrogenases
JF  - PLoS one
N2  - The maturation of bacterial molybdoenzymes is a complex process leading to the insertion of the bulky bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor into the apoenzyme. Most molybdoenzymes were shown to contain a specific chaperone for the insertion of the bis-MGD cofactor. Formate dehydrogenases (FDH) together with their molecular chaperone partner seem to display an exception to this specificity rule, since the chaperone FdhD has been proven to be involved in the maturation of all three FDH enzymes present in Escherichia colt. Multiple roles have been suggested for FdhD-like chaperones in the past, including the involvement in a sulfur transfer reaction from the L-cysteine desulfurase IscS to bis-MGD by the action of two cysteine residues present in a conserved CXXC motif of the chaperones. However, in this study we show by phylogenetic analyses that the CXXC motif is not conserved among FdhD-like chaperones. We compared in detail the FdhD-like homologues from Rhodobacter capsulatus and E. colt and show that their roles in the maturation of FDH enzymes from different subgroups can be exchanged. We reveal that bis-MGDbinding is a common characteristic of FdhD-like proteins and that the cofactor is bound with a sulfido-ligand at the molybdenum atom to the chaperone. Generally, we reveal that the cysteine residues in the motif CXXC of the chaperone are not essential for the production of active FDH enzymes.
Y1  - 2018
U6  - https://doi.org/10.1371/journal.pone.0201935
SN  - 1932-6203
VL  - 13
IS  - 11
PB  - PLoS
CY  - San Fransisco
ER  - 
TY  - JOUR
A1  - Rosenbaum, Benjamin
A1  - Raatz, Michael
A1  - Weithoff, Guntram
A1  - Fussmann, Gregor F.
A1  - Gaedke, Ursula
T1  - Estimating parameters from multiple time series of population dynamics using bayesian inference
JF  - Frontiers in ecology and evolution
N2  - Empirical time series of interacting entities, e.g., species abundances, are highly useful to study ecological mechanisms. Mathematical models are valuable tools to further elucidate those mechanisms and underlying processes. However, obtaining an agreement between model predictions and experimental observations remains a demanding task. As models always abstract from reality one parameter often summarizes several properties. Parameter measurements are performed in additional experiments independent of the ones delivering the time series. Transferring these parameter values to different settings may result in incorrect parametrizations. On top of that, the properties of organisms and thus the respective parameter values may vary considerably. These issues limit the use of a priori model parametrizations. In this study, we present a method suited for a direct estimation of model parameters and their variability from experimental time series data. We combine numerical simulations of a continuous-time dynamical population model with Bayesian inference, using a hierarchical framework that allows for variability of individual parameters. The method is applied to a comprehensive set of time series from a laboratory predator-prey system that features both steady states and cyclic population dynamics. Our model predictions are able to reproduce both steady states and cyclic dynamics of the data. Additionally to the direct estimates of the parameter values, the Bayesian approach also provides their uncertainties. We found that fitting cyclic population dynamics, which contain more information on the process rates than steady states, yields more precise parameter estimates. We detected significant variability among parameters of different time series and identified the variation in the maximum growth rate of the prey as a source for the transition from steady states to cyclic dynamics. By lending more flexibility to the model, our approach facilitates parametrizations and shows more easily which patterns in time series can be explained also by simple models. Applying Bayesian inference and dynamical population models in conjunction may help to quantify the profound variability in organismal properties in nature.
KW  - Bayesian inference
KW  - chemostat experiments
KW  - ordinary differential equation
KW  - parameter estimation
KW  - population dynamics
KW  - predator prey
KW  - time series analysis
KW  - trait variability
Y1  - 2019
U6  - https://doi.org/10.3389/fevo.2018.00234
SN  - 2296-701X
VL  - 6
PB  - Frontiers Research Foundation
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Kruse, Julia
A1  - Kummer, Volker
A1  - Shivas, Roger G.
A1  - Thines, Marco
T1  - The first smut fungus, Thecaphora anthemidis sp nov (Glomosporiaceae), described from Anthemis (Asteraceae)
JF  - MycoKeys
N2  - There are 63 known species of Thecaphora (Glomosporiaceae, Ustilaginomycotina), a third of which occur on Asteraceae. These smut fungi produce yellowish-brown to reddish-brown masses of spore balls in specific, mostly regenerative, plant organs. A species of Thecaphora was collected in the flower heads of Anthemis chia (Anthemideae, Asteraceae) on Rhodes Island, Greece, in 2015 and 2017, which represents the first smut record of a smut fungus on a host plant species in this tribe. Based on its distinctive morphology, host species and genetic divergence, this species is described as Thecaphora anthemidis sp. nov. Molecular barcodes of the ITS region are provided for this and several other species of Thecaphora. A phylogenetic and morphological comparison to closely related species showed that Th. anthemidis differed from other species of Thecaphora. Thecaphora anthemidis produced loose spore balls in the flower heads and peduncles of Anthemis chia unlike other flower-infecting species.
KW  - Glomosporiaceae
KW  - host specificity
KW  - internal transcribed spacer
KW  - molecular phylogenetics
KW  - smut fungi
Y1  - 2018
U6  - https://doi.org/10.3897/mycokeys.41.28454
SN  - 1314-4057
SN  - 1314-4049
IS  - 41
SP  - 39
EP  - 50
PB  - Pensoft Publ.
CY  - Sofia
ER  - 
TY  - JOUR
A1  - Perkins, Daniel M.
A1  - Perna, Andrea
A1  - Adrian, Rita
A1  - Cermeno, Pedro
A1  - Gaedke, Ursula
A1  - Huete-Ortega, Maria
A1  - White, Ethan P.
A1  - Yvon-Durocher, Gabriel
T1  - Energetic equivalence underpins the size structure of tree and phytoplankton communities
JF  - Nature Communications
N2  - The size structure of autotroph communities - the relative abundance of small vs. large individuals - shapes the functioning of ecosystems. Whether common mechanisms underpin the size structure of unicellular and multicellular autotrophs is, however, unknown. Using a global data compilation, we show that individual body masses in tree and phytoplankton communities follow power-law distributions and that the average exponents of these individual size distributions (ISD) differ. Phytoplankton communities are characterized by an average ISD exponent consistent with three-quarter-power scaling of metabolism with body mass and equivalence in energy use among mass classes. Tree communities deviate from this pattern in a manner consistent with equivalence in energy use among diameter size classes. Our findings suggest that whilst universal metabolic constraints ultimately underlie the emergent size structure of autotroph communities, divergent aspects of body size (volumetric vs. linear dimensions) shape the ecological outcome of metabolic scaling in forest vs. pelagic ecosystems.
Y1  - 2019
U6  - https://doi.org/10.1038/s41467-018-08039-3
SN  - 2041-1723
VL  - 10
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Thomas, Jessica E.
A1  - Carvalho, Gary R.
A1  - Haile, James
A1  - Rawlence, Nicolas J.
A1  - Martin, Michael D.
A1  - Ho, Simon Y. W.
A1  - Sigfusson, Arnor P.
A1  - Josefsson, Vigfus A.
A1  - Frederiksen, Morten
A1  - Linnebjerg, Jannie F.
A1  - Castruita, Jose A. Samaniego
A1  - Niemann, Jonas
A1  - Sinding, Mikkel-Holger S.
A1  - Sandoval-Velasco, Marcela
A1  - Soares, Andre E. R.
A1  - Lacy, Robert
A1  - Barilaro, Christina
A1  - Best, Juila
A1  - Brandis, Dirk
A1  - Cavallo, Chiara
A1  - Elorza, Mikelo
A1  - Garrett, Kimball L.
A1  - Groot, Maaike
A1  - Johansson, Friederike
A1  - Lifjeld, Jan T.
A1  - Nilson, Goran
A1  - Serjeanston, Dale
A1  - Sweet, Paul
A1  - Fuller, Errol
A1  - Hufthammer, Anne Karin
A1  - Meldgaard, Morten
A1  - Fjeldsa, Jon
A1  - Shapiro, Beth
A1  - Hofreiter, Michael
A1  - Stewart, John R.
A1  - Gilbert, M. Thomas P.
A1  - Knapp, Michael
T1  - Demographic reconstruction from ancient DNA supports rapid extinction of the great auk
JF  - eLife
N2  - The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.
Y1  - 2019
U6  - https://doi.org/10.7554/eLife.47509
SN  - 2050-084X
VL  - 8
PB  - eLife Sciences Publications
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Bröker, Katharine
A1  - Sinelnikov, Evgeny
A1  - Gustavus, Dirk
A1  - Schumacher, Udo
A1  - Pörtner, Ralf
A1  - Hoffmeister, Hans
A1  - Lüth, Stefan
A1  - Dammermann, Werner
T1  - Mass Production of Highly Active NK Cells for Cancer Immunotherapy in a GMP Conform Perfusion Bioreactor
JF  - Frontiers in Bioengineering and Biotechnology
N2  - NK cells have emerged as promising candidates for cancer immunotherapy, especially due to their ability to fight circulating tumor cells thereby preventing metastases formation. Hence several studies have been performed to generate and expand highly cytotoxic NK cells ex vivo, e.g., by using specific cytokines to upregulate both their proliferation and surface expression of distinct activating receptors. Apart from an enhanced activity, application of NK cells as immunotherapeutic agent further requires sufficient cell numbers and a high purity. All these parameters depend on a variety of different factors including the starting material, additives like cytokines as well as the culture system. Here we analyzed PBMC-derived NK cells of five anonymized healthy donors expanded under specific conditions in an innovative perfusion bioreactor system with respect to their phenotype, IFN gamma production, and cytotoxicity in vitro. Important features of the meander type bioreactors used here are a directed laminar flow of medium and control of relevant process parameters. Cells are cultivated under "steady state" conditions in perfusion mode. Our data demonstrate that expansion of CD3(+) T cell depleted PBMCs in our standardized system generates massive amounts of highly pure (>85%) and potent anticancer active NK cells. These cells express a variety of important receptors driving NK cell recruitment, adhesion as well as activation. More specifically, they express the chemokine receptors CXCR3, CXCR4, and CCR7, the adhesion molecules L-selectin, LFA-1, and VLA-4, the activating receptors NKp30, NKp44, NKp46, NKG2D, DNAM1, and CD16 as well as the death ligands TRAIL and Fas-L. Moreover, the generated NK cells show a strong IFN gamma expression upon cultivation with K562 tumor cells and demonstrate a high cytotoxicity toward leukemic as well as solid tumor cell lines in vitro. Altogether, these characteristics promise a high clinical potency of thus produced NK cells awaiting further evaluation.
KW  - natural killer cells (NK cells)
KW  - cytotoxicity
KW  - tumor immunity
KW  - immunotherapy
KW  - perfusion bioreactor
KW  - GMP
KW  - mass production process
Y1  - 2019
U6  - https://doi.org/10.3389/fbioe.2019.00194
SN  - 2296-4185
VL  - 7
PB  - Frontiers Research Foundation
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Miele, Vincent
A1  - Guill, Christian
A1  - Ramos-Jiliberto, Rodrigo
A1  - Kéfi, Sonia
T1  - Non-trophic interactions strengthen the diversity-functioning relationship in an ecological bioenergetic network model
JF  - PLoS Computational Biology : a new community journal
N2  - Ecological communities are undeniably diverse, both in terms of the species that compose them as well as the type of interactions that link species to each other. Despite this long recognition of the coexistence of multiple interaction types in nature, little is known about the consequences of this diversity for community functioning. In the ongoing context of global change and increasing species extinction rates, it seems crucial to improve our understanding of the drivers of the relationship between species diversity and ecosystem functioning. Here, using a multispecies dynamical model of ecological communities including various interaction types (e.g. competition for space, predator interference, recruitment facilitation in addition to feeding), we studied the role of the presence and the intensity of these interactions for species diversity, community functioning (biomass and production) and the relationship between diversity and functioning. Taken jointly, the diverse interactions have significant effects on species diversity, whose amplitude and sign depend on the type of interactions involved and their relative abundance. They however consistently increase the slope of the relationship between diversity and functioning, suggesting that species losses might have stronger effects on community functioning than expected when ignoring the diversity of interaction types and focusing on feeding interactions only.
Y1  - 2020
U6  - https://doi.org/10.1371/journal.pcbi.1007269
SN  - 1553-7358
VL  - 15
IS  - 8
PB  - PLoS
CY  - San Fransisco
ER  - 
TY  - JOUR
A1  - Rieck, Christoph Paul Kurt
A1  - Geiger, Daniel
A1  - Munkert, Jennifer
A1  - Messerschmidt, Katrin
A1  - Petersen, Jan
A1  - Strasser, Juliane
A1  - Meitinger, Nadine
A1  - Kreis, Wolfgang
T1  - Biosynthetic approach to combine the first steps of cardenolide formation in Saccharomyces cerevisiae
JF  - Microbiologyopen
N2  - A yeast expression plasmid was constructed containing a cardenolide biosynthetic module, referred to as CARD II, using the AssemblX toolkit, which enables the assembly of large DNA constructs. The genes cloned into the vector were (a) a Δ5‐3β‐hydroxysteroid dehydrogenase gene from Digitalis lanata, (b) a steroid Δ5‐isomerase gene from Comamonas testosteronii, (c) a mutated steroid‐5β‐reductase gene from Arabidopsis thaliana, and (d) a steroid 21‐hydroxylase gene from Mus musculus. A second plasmid bearing an ADR/ADX fusion gene from Bos taurus was also constructed. A Saccharomyces cerevisiae strain bearing these two plasmids was generated. This strain, termed “CARD II yeast”, was capable of producing 5β‐pregnane‐3β,21‐diol‐20‐one, a central intermediate in 5β‐cardenolide biosynthesis, starting from pregnenolone which was added to the culture medium. Using this approach, five consecutive steps in cardenolide biosynthesis were realized in baker's yeast.
Y1  - 2019
U6  - https://doi.org/10.1002/mbo3.925
SN  - 2045-8827
VL  - 8
IS  - 12
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Werger, Luise
A1  - Bergmann, Joana
A1  - Weber, Ewald
A1  - Heinze, Johannes
T1  - Wind intensity affects fine root morphological traits with consequences for plant-soil feedback effects
JF  - Annals of Botany Plants
N2  - Wind influences the development, architecture and morphology of plant roots and may modify subsequent interactions between plants and soil (plant–soil feedbacks—PSFs). However, information on wind effects on fine root morphology is scarce and the extent to which wind changes plant–soil interactions remains unclear. Therefore, we investigated the effects of two wind intensity levels by manipulating surrounding vegetation height in a grassland PSF field experiment. We grew four common plant species (two grasses and two non-leguminous forbs) with soil biota either previously conditioned by these or other species and tested the effect of wind on root:shoot ratio, fine root morphological traits as well as the outcome for PSFs. Wind intensity did not affect biomass allocation (i.e. root:shoot ratio) in any species. However, fine-root morphology of all species changed under high wind intensity. High wind intensity increased specific root length and surface area and decreased root tissue density, especially in the two grasses. Similarly, the direction of PSFs changed under high wind intensity in all four species, but differences in biomass production on the different soils between high and low wind intensity were marginal and most pronounced when comparing grasses with forbs. Because soils did not differ in plant-available nor total nutrient content, the results suggest that wind-induced changes in root morphology have the potential to influence plant–soil interactions. Linking wind-induced changes in fine-root morphology to effects on PSF improves our understanding of plant–soil interactions under changing environmental conditions.
KW  - Wind
KW  - root traits
KW  - root morphology
KW  - specific root length
KW  - plant–soil feedback
Y1  - 2020
U6  - https://doi.org/10.1093/aobpla/plaa050
SN  - 2041-2851
VL  - 12
IS  - 5
PB  - Oxford University Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - He, Hai
A1  - Höper, Rune
A1  - Dodenhöft, Moritz
A1  - Marlière, Philippe
A1  - Bar-Even, Arren
T1  - An optimized methanol assimilation pathway relying on promiscuous formaldehyde-condensing aldolases in E. coli
JF  - Metabolic Engineering
N2  - Engineering biotechnological microorganisms to use methanol as a feedstock for bioproduction is a major goal for the synthetic metabolism community. Here, we aim to redesign the natural serine cycle for implementation in E. coli. We propose the homoserine cycle, relying on two promiscuous formaldehyde aldolase reactions, as a superior pathway design. The homoserine cycle is expected to outperform the serine cycle and its variants with respect to biomass yield, thermodynamic favorability, and integration with host endogenous metabolism. Even as compared to the RuMP cycle, the most efficient naturally occurring methanol assimilation route, the homoserine cycle is expected to support higher yields of a wide array of products. We test the in vivo feasibility of the homoserine cycle by constructing several E. coli gene deletion strains whose growth is coupled to the activity of different pathway segments. Using this approach, we demonstrate that all required promiscuous enzymes are active enough to enable growth of the auxotrophic strains. Our findings thus identify a novel metabolic solution that opens the way to an optimized methylotrophic platform.
KW  - Pathway design
KW  - Promiscuous enzymes
KW  - Formaldehyde assimilation
KW  - Serine cycle
KW  - Growth selection
Y1  - 2020
U6  - https://doi.org/10.1016/j.ymben.2020.03.002
SN  - 1096-7176
SN  - 1096-7184
VL  - 60
SP  - 1
EP  - 13
PB  - Elsevier
CY  - Amsterdam [u.a.]
ER  - 
TY  - JOUR
A1  - He, Hai
A1  - Noor, Elad
A1  - Ramos-Parra, Perla A.
A1  - García-Valencia, Liliana E.
A1  - Patterson, Jenelle A.
A1  - Díaz de la Garza, Rocío I.
A1  - Hanson, Andrew D.
A1  - Bar-Even, Arren
T1  - In Vivo Rate of Formaldehyde Condensation with Tetrahydrofolate
JF  - Metabolites
N2  - Formaldehyde is a highly reactive compound that participates in multiple spontaneous reactions, but these are mostly deleterious and damage cellular components. In contrast, the spontaneous condensation of formaldehyde with tetrahydrofolate (THF) has been proposed to contribute to the assimilation of this intermediate during growth on C1 carbon sources such as methanol. However, the in vivo rate of this condensation reaction is unknown and its possible contribution to growth remains elusive. Here, we used microbial platforms to assess the rate of this condensation in the cellular environment. We constructed Escherichia coli strains lacking the enzymes that naturally produce 5,10-methylene-THF. These strains were able to grow on minimal medium only when equipped with a sarcosine (N-methyl-glycine) oxidation pathway that sustained a high cellular concentration of formaldehyde, which spontaneously reacts with THF to produce 5,10-methylene-THF. We used flux balance analysis to derive the rate of the spontaneous condensation from the observed growth rate. According to this, we calculated that a microorganism obtaining its entire biomass via the spontaneous condensation of formaldehyde with THF would have a doubling time of more than three weeks. Hence, this spontaneous reaction is unlikely to serve as an effective route for formaldehyde assimilation.
KW  - one-carbon metabolism
KW  - spontaneous reaction
KW  - auxotrophy
KW  - serine cycle
KW  - phenotypic phase plane
Y1  - 2019
U6  - https://doi.org/10.3390/metabo10020065
SN  - 2218-1989
VL  - 10
IS  - 65
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Schiro, Gabriele
A1  - Colangeli, Pierluigi
A1  - Müller, Marina E. H.
T1  - A Metabarcoding Analysis of the Mycobiome of Wheat Ears Across a Topographically Heterogeneous Field
JF  - Frontiers in microbiology
KW  - Fusarium
KW  - microclimate
KW  - canopy
KW  - fungal community
KW  - Alternaria
KW  - spatially induced variance
Y1  - 2019
U6  - https://doi.org/10.3389/fmicb.2019.02095
SN  - 1664-302X
VL  - 10
PB  - Frontiers Research Foundation
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Brust, Henrike
A1  - Orzechowski, Slawomir
A1  - Fettke, Jörg
T1  - Starch and Glycogen Analyses
BT  - Methods and Techniques
JF  - Biomolecules
N2  - For complex carbohydrates, such as glycogen and starch, various analytical methods and techniques exist allowing the detailed characterization of these storage carbohydrates. In this article, we give a brief overview of the most frequently used methods, techniques, and results. Furthermore, we give insights in the isolation, purification, and fragmentation of both starch and glycogen. An overview of the different structural levels of the glucans is given and the corresponding analytical techniques are discussed. Moreover, future perspectives of the analytical needs and the challenges of the currently developing scientific questions are included
KW  - starch
KW  - glycogen
KW  - analytics
Y1  - 2020
U6  - https://doi.org/10.3390/biom10071020
SN  - 2218-273X
VL  - 10
IS  - 7
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Ozcelikay, Goksu
A1  - Kurbanoglu, Sevinc
A1  - Zhang, Xiaorong
A1  - Söz, Çağla Kosak
A1  - Wollenberger, Ulla
A1  - Ozkan, Sibel A.
A1  - Yarman, Aysu
A1  - Scheller, Frieder W.
T1  - Electrochemical MIP Sensor for Butyrylcholinesterase
JF  - Polymers
N2  - Molecularly imprinted polymers (MIPs) mimic the binding sites of antibodies by substituting the amino acid-scaffold of proteins by synthetic polymers. In this work, the first MIP for the recognition of the diagnostically relevant enzyme butyrylcholinesterase (BuChE) is presented. The MIP was prepared using electropolymerization of the functional monomer o-phenylenediamine and was deposited as a thin film on a glassy carbon electrode by oxidative potentiodynamic polymerization. Rebinding and removal of the template were detected by cyclic voltammetry using ferricyanide as a redox marker. Furthermore, the enzymatic activity of BuChE rebound to the MIP was measured via the anodic oxidation of thiocholine, the reaction product of butyrylthiocholine. The response was linear between 50 pM and 2 nM concentrations of BuChE with a detection limit of 14.7 pM. In addition to the high sensitivity for BuChE, the sensor responded towards pseudo-irreversible inhibitors in the lower mM range.
KW  - molecularly imprinted polymers
KW  - biomimetic sensors
KW  - butyrylcholinesterase
KW  - o-phenylenediamine
KW  - rivastigmine
Y1  - 2019
U6  - https://doi.org/10.3390/polym11121970
SN  - 2073-4360
VL  - 11
IS  - 12
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Fritze, Marcus
A1  - Costantini, David
A1  - Fickel, Jörns
A1  - Wehner, Dana
A1  - Czirjak, Gsbor A.
A1  - Voigt, Christian Claus
T1  - Immune response of hibernating European bats to a fungal challenge
JF  - Biology open
N2  - Immunological responses of hibernating mammals are suppressed at low body temperatures, a possible explanation for the devastating effect of the white-nose syndrome on hibernating North American bats. However, European bats seem to cope well with the fungal causative agent of the disease. To better understand the immune response of hibernating bats, especially against fungal pathogens, we challenged European greater mouse-eared bats (Myotis myotis) by inoculating the fungal antigen zymosan. We monitored torpor patterns, immune gene expressions, different aspects of the acute phase response and plasma oxidative status markers, and compared them with sham-injected control animals at 30 min, 48 h and 96 h after inoculation. Torpor patterns, body temperatures, body masses, white blood cell counts, expression of immune genes, reactive oxygen metabolites and non-enzymatic antioxidant capacity did not differ between groups during the experiment. However, zymosan injected bats had significantly higher levels of haptoglobin than the control animals. Our results indicate that hibernating greater mouse-eared bats mount an inflammatory response to a fungal challenge, with only mild to negligible consequences for the energy budget of hibernation. Our study gives a first hint that hibernating European bats may have evolved a hibernation-adjusted immune response in order to balance the trade-off between competent pathogen elimination and a prudent energy-saving regime.
KW  - Fungal challenge
KW  - Torpor
KW  - Body temperature
KW  - Zymosan
KW  - Acute phase response
KW  - Oxidative stress
KW  - Myotis myotis
Y1  - 2019
U6  - https://doi.org/10.1242/bio.046078
SN  - 2046-6390
VL  - 8
IS  - 10
PB  - Company biologists ltd
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Rossberg, Axel G.
A1  - Gaedke, Ursula
A1  - Kratina, Pavel
T1  - Dome patterns in pelagic size spectra reveal strong trophic cascades
JF  - Nature Communications
N2  - In ecological communities, especially the pelagic zones of aquatic ecosystems, certain bodysize ranges are often over-represented compared to others. Community size spectra, the distributions of community biomass over the logarithmic body-mass axis, tend to exhibit regularly spaced local maxima, called "domes", separated by steep troughs. Contrasting established theory, we explain these dome patterns as manifestations of top-down trophic cascades along aquatic food chains. Compiling high quality size-spectrum data and comparing these with a size-spectrum model introduced in this study, we test this theory and develop a detailed picture of the mechanisms by which bottom-up and top-down effects interact to generate dome patterns. Results imply that strong top-down trophic cascades are common in freshwater communities, much more than hitherto demonstrated, and may arise in nutrient rich marine systems as well. Transferring insights from the general theory of nonlinear pattern formation to domes patterns, we provide new interpretations of past lake-manipulation experiments.
Y1  - 2019
U6  - https://doi.org/10.1038/s41467-019-12289-0
SN  - 2041-1723
VL  - 10
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Matthey-Doret, Cyril
A1  - van der Kooi, Casper J.
A1  - Jeffries, Daniel L.
A1  - Bast, Jens
A1  - Dennis, Alice B.
A1  - Vorburger, Christoph
A1  - Schwander, Tanja
T1  - Mapping of Multiple Complementary Sex Determination Loci in a Parasitoid Wasp
JF  - Genome biology and evolution
N2  - Sex determination has evolved in a variety of ways and can depend on environmental and genetic signals. A widespread form of genetic sex determination is haplodiploidy, where unfertilized, haploid eggs develop into males and fertilized diploid eggs into females. One of the molecular mechanisms underlying haplodiploidy in Hymenoptera, the large insect order comprising ants, bees, and wasps, is complementary sex determination (CSD). In species with CSD, heterozygosity at one or several loci induces female development. Here, we identify the genomic regions putatively underlying multilocus CSD in the parasitoid wasp Lysiphlebus fabarum using restriction -site associated DNA sequencing. By analyzing segregation patterns at polymorphic sites among 331 diploid males and females, we identify up to four CSD candidate regions, all on different chromosomes. None of the candidate regions feature evidence for homology with the csd gene from the honey bee, the only species in which CSD has been characterized, suggesting that CSD in L. fabarum is regulated via a novel molecular mechanism. Moreover, no homology is shared between the candidate loci, in contrast to the idea that multilocus CSD should emerge from duplications of an ancestral single -locus system. Taken together, our results suggest that the molecular mechanisms underlying CSD in Hymenoptera are not conserved between species, raising the question as to whether CSD may have evolved multiple times independently in the group.
KW  - hymenoptera
KW  - sex determination
KW  - Lysiphlebus fabarum
KW  - CSD
Y1  - 2019
U6  - https://doi.org/10.1093/gbe/evz219
SN  - 1759-6653
VL  - 11
IS  - 10
SP  - 2954
EP  - 2962
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Drago, Claudia
A1  - Pawlak, Julia
A1  - Weithoff, Guntram
T1  - Biogenic aggregation of small microplastics alters their ingestion by a common freshwater micro-invertebrate
JF  - Frontiers in Environmental Science
N2  - In recent years, increasing concerns have been raised about the environmental risk of microplastics in freshwater ecosystems. Small microplastics enter the water either directly or accumulate through disintegration of larger plastic particles. These particles might then be ingested by filter-feeding zooplankton, such as rotifers. Particles released into the water may also interact with the biota through the formation of aggregates, which might alter the uptake by zooplankton. In this study, we tested for size-specific aggregation of polystyrene microspheres and their ingestion by a common freshwater rotifer Brachionus calyciflorus. The ingestion of three sizes of polystyrene microspheres (MS) 1-, 3-, and 6-mu m was investigated. Each MS size was tested in combination with three different treatments: MS as the sole food intake, MS in association with food algae and MS aggregated with biogenic matter. After 72 h incubation in pre-filtered natural river water, the majority of the 1-mu m spheres occurred as aggregates. The larger the particles, the higher the relative number of single particles and the larger the aggregates. All particles were ingested by the rotifer following a Type-II functional response. The presence of algae did not influence the ingestion of the MS for all three sizes. The biogenic aggregation of microspheres led to a significant size-dependent alteration in their ingestion. Rotifers ingested more microspheres (MS) when exposed to aggregated 1- and 3-mu m MS as compared to single spheres, whereas fewer aggregated 6-mu m spheres were ingested. This indicates that the small particles when aggregated were in an effective size range for Brachionus, while the aggregated larger spheres became too large to be efficiently ingested. These observations provide the first evidence of a size- and aggregation-dependent feeding interaction between microplastics and rotifers. Microplastics when aggregated with biogenic particles in a natural environment can rapidly change their size-dependent availability. The aggregation properties of microplastics should be taken into account when performing experiments mimicking the natural environment.
KW  - microplastics ingestion
KW  - Brachionus calyciflorus
KW  - aggregation
KW  - microplastics
KW  - polystyrene
KW  - functional response
Y1  - 2020
U6  - https://doi.org/10.3389/fenvs.2020.574274
SN  - 2296-665X
VL  - 8
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Ogunkola, Moses Olalekan
A1  - Guiraudie-Capraz, Gaelle
A1  - Féron, François
A1  - Leimkühler, Silke
T1  - The Human Mercaptopyruvate Sulfurtransferase TUM1 Is Involved in Moco Biosynthesis, Cytosolic tRNA Thiolation and Cellular Bioenergetics in Human Embryonic Kidney Cells
JF  - Biomolecules
N2  - Sulfur is an important element that is incorporated into many biomolecules in humans. The incorporation and transfer of sulfur into biomolecules is, however, facilitated by a series of different sulfurtransferases. Among these sulfurtransferases is the human mercaptopyruvate sulfurtransferase (MPST) also designated as tRNA thiouridine modification protein (TUM1). The role of the human TUM1 protein has been suggested in a wide range of physiological processes in the cell among which are but not limited to involvement in Molybdenum cofactor (Moco) biosynthesis, cytosolic tRNA thiolation and generation of H2S as signaling molecule both in mitochondria and the cytosol. Previous interaction studies showed that TUM1 interacts with the L-cysteine desulfurase NFS1 and the Molybdenum cofactor biosynthesis protein 3 (MOCS3). Here, we show the roles of TUM1 in human cells using CRISPR/Cas9 genetically modified Human Embryonic Kidney cells. Here, we show that TUM1 is involved in the sulfur transfer for Molybdenum cofactor synthesis and tRNA thiomodification by spectrophotometric measurement of the activity of sulfite oxidase and liquid chromatography quantification of the level of sulfur-modified tRNA. Further, we show that TUM1 has a role in hydrogen sulfide production and cellular bioenergetics.
KW  - Moco biosynthesis
KW  - sulfite oxidase
KW  - cytosolic tRNA thiolation
KW  - 5-methoxycarbonylmethyl-2-thiouridine
KW  - H2S biosynthesis
KW  - cellular bioenergetics
Y1  - 2023
U6  - https://doi.org/10.3390/biom13010144
SN  - 2218-273X
VL  - 13
SP  - 1
EP  - 23
PB  - MDPI
CY  - Basel, Schweiz
ET  - 1
ER  - 
TY  - JOUR
A1  - Marggraf, Lara Christin
A1  - Lindecke, Oliver
A1  - Voigt, Christian C.
A1  - Pētersons, Gunārs
A1  - Voigt-Heucke, Silke Luise
T1  - Nathusius’ bats, Pipistrellus nathusii, bypass mating opportunities of their own species, but respond to foraging heterospecifics on migratory transit flights
JF  - Frontiers in Ecology and Evolution
N2  - In late summer, migratory bats of the temperate zone face the challenge of accomplishing two energy-demanding tasks almost at the same time: migration and mating. Both require information and involve search efforts, such as localizing prey or finding potential mates. In non-migrating bat species, playback studies showed that listening to vocalizations of other bats, both con-and heterospecifics, may help a recipient bat to find foraging patches and mating sites. However, we are still unaware of the degree to which migrating bats depend on con-or heterospecific vocalizations for identifying potential feeding or mating opportunities during nightly transit flights. Here, we investigated the vocal responses of Nathusius’ pipistrelle bats, Pipistrellus nathusii, to simulated feeding and courtship aggregations at a coastal migration corridor. We presented migrating bats either feeding buzzes or courtship calls of their own or a heterospecific migratory species, the common noctule, Nyctalus noctula. We expected that during migratory transit flights, simulated feeding opportunities would be particularly attractive to bats, as well as simulated mating opportunities which may indicate suitable roosts for a stopover. However, we found that when compared to the natural silence of both pre-and post-playback phases, bats called indifferently during the playback of conspecific feeding sounds, whereas P. nathusii echolocation call activity increased during simulated feeding of N. noctula. In contrast, the call activity of P. nathusii decreased during the playback of conspecific courtship calls, while no response could be detected when heterospecific call types were broadcasted. Our results suggest that while on migratory transits, P. nathusii circumnavigate conspecific mating aggregations, possibly to save time or to reduce the risks associated with social interactions where aggression due to territoriality might be expected. This avoidance behavior could be a result of optimization strategies by P. nathusii when performing long-distance migratory flights, and it could also explain the lack of a response to simulated conspecific feeding. However, the observed increase of activity in response to simulated feeding of N. noctula, suggests that P. nathusii individuals may be eavesdropping on other aerial hawking insectivorous species during migration, especially if these occupy a slightly different foraging niche.
KW  - playback
KW  - phonotaxis
KW  - bats
KW  - acoustic communication
KW  - animal migration
KW  - eavesdropping
KW  - echolocation
KW  - Pipistrellus nathusii
Y1  - 2023
U6  - https://doi.org/10.3389/fevo.2022.908560
SN  - 2296-701X
SP  - 1
EP  - 10
PB  - Frontiers
CY  - Lausanne, Schweiz
ER  - 
TY  - JOUR
A1  - Wojcik, Laurie Anne
A1  - Ceulemans, Ruben
A1  - Gaedke, Ursula
T1  - Functional diversity buffers the effects of a pulse perturbation on the dynamics of tritrophic food webs
JF  - Ecology and Evolution
N2  - Biodiversity decline causes a loss of functional diversity, which threatens ecosystems through a dangerous feedback loop: This loss may hamper ecosystems’ ability to buffer environmental changes, leading to further biodiversity losses. In this context, the increasing frequency of human-induced excessive loading of nutrients causes major problems in aquatic systems. Previous studies investigating how functional diversity influences the response of food webs to disturbances have mainly considered systems with at most two functionally diverse trophic levels. We investigated the effects of functional diversity on the robustness, that is, resistance, resilience, and elasticity, using a tritrophic—and thus more realistic—plankton food web model. We compared a non-adaptive food chain with no diversity within the individual trophic levels to a more diverse food web with three adaptive trophic levels. The species fitness differences were balanced through trade-offs between defense/growth rate for prey and selectivity/half-saturation constant for predators. We showed that the resistance, resilience, and elasticity of tritrophic food webs decreased with larger perturbation sizes and depended on the state of the system when the perturbation occurred. Importantly, we found that a more diverse food web was generally more resistant and resilient but its elasticity was context-dependent. Particularly, functional diversity reduced the probability of a regime shift toward a non-desirable alternative state. The basal-intermediate interaction consistently determined the robustness against a nutrient pulse despite the complex influence of the shape and type of the dynamical attractors. This relationship was strongly influenced by the diversity present and the third trophic level. Overall, using a food web model of realistic complexity, this study confirms the destructive potential of the positive feedback loop between biodiversity loss and robustness, by uncovering mechanisms leading to a decrease in resistance, resilience, and potentially elasticity as functional diversity declines.
KW  - functional diversity
KW  - nutrient spike
KW  - pulse perturbation
KW  - regime shift
KW  - robustness
KW  - tritrophic food web
Y1  - 2021
U6  - https://doi.org/10.1002/ece3.8214
SN  - 2045-7758
N1  - Wojcik and Ceulemans shared first authorship.
VL  - 11
IS  - 22
SP  - 15639
EP  - 15663
PB  - John Wiley & Sons, Inc.
CY  - Hoboken (New Jersey)
ER  - 
TY  - JOUR
A1  - Endesfelder, Stefanie
A1  - Weichelt, Ulrike
A1  - Strauß, Evelyn
A1  - Schlör, Anja
A1  - Sifringer, Marco
A1  - Scheuer, Till
A1  - Bührer, Christoph
A1  - Schmitz, Thomas
T1  - Neuroprotection by caffeine in hyperoxia-induced neonatal brain injury
JF  - International journal of molecular sciences
N2  - Sequelae of prematurity triggered by oxidative stress and free radical-mediated tissue damage have coined the term “oxygen radical disease of prematurity”. Caffeine, a potent free radical scavenger and adenosine receptor antagonist, reduces rates of brain damage in preterm infants. In the present study, we investigated the effects of caffeine on oxidative stress markers, anti-oxidative response, inflammation, redox-sensitive transcription factors, apoptosis, and extracellular matrix following the induction of hyperoxia in neonatal rats. The brain of a rat pups at postnatal Day 6 (P6) corresponds to that of a human fetal brain at 28–32 weeks gestation and the neonatal rat is an ideal model in which to investigate effects of oxidative stress and neuroprotection of caffeine on the developing brain. Six-day-old Wistar rats were pre-treated with caffeine and exposed to 80% oxygen for 24 and 48 h. Caffeine reduced oxidative stress marker (heme oxygenase-1, lipid peroxidation, hydrogen peroxide, and glutamate-cysteine ligase catalytic subunit (GCLC)), promoted anti-oxidative response (superoxide dismutase, peroxiredoxin 1, and sulfiredoxin 1), down-regulated pro-inflammatory cytokines, modulated redox-sensitive transcription factor expression (Nrf2/Keap1, and NFκB), reduced pro-apoptotic effectors (poly (ADP-ribose) polymerase-1 (PARP-1), apoptosis inducing factor (AIF), and caspase-3), and diminished extracellular matrix degeneration (matrix metalloproteinases (MMP) 2, and inhibitor of metalloproteinase (TIMP) 1/2). Our study affirms that caffeine is a pleiotropic neuroprotective drug in the developing brain due to its anti-oxidant, anti-inflammatory, and anti-apoptotic properties.
KW  - anti-oxidative response
KW  - caffeine
KW  - hyperoxia
KW  - oxidative stress
KW  - preterm infants
KW  - developing brain
Y1  - 2017
U6  - https://doi.org/10.3390/ijms18010187
SN  - 1422-0067
SN  - 1661-6596
VL  - 18
PB  - Molecular Diversity Preservation International
CY  - Basel
ER  - 
TY  - JOUR
A1  - Reeg, Jette
A1  - Strigl, Lea
A1  - Jeltsch, Florian
T1  - Agricultural buffer zone thresholds to safeguard functional bee diversity
BT  - Insights from a community modeling approach
JF  - Ecology and Evolution
N2  - Wild bee species are important pollinators in agricultural landscapes. However, population decline was reported over the last decades and is still ongoing. While agricultural intensification is a major driver of the rapid loss of pollinating species, transition zones between arable fields and forest or grassland patches, i.e., agricultural buffer zones, are frequently mentioned as suitable mitigation measures to support wild bee populations and other pollinator species. Despite the reported general positive effect, it remains unclear which amount of buffer zones is needed to ensure a sustainable and permanent impact for enhancing bee diversity and abundance. To address this question at a pollinator community level, we implemented a process-based, spatially explicit simulation model of functional bee diversity dynamics in an agricultural landscape. More specifically, we introduced a variable amount of agricultural buffer zones (ABZs) at the transition of arable to grassland, or arable to forest patches to analyze the impact on bee functional diversity and functional richness. We focused our study on solitary bees in a typical agricultural area in the Northeast of Germany. Our results showed positive effects with at least 25% of virtually implemented agricultural buffer zones. However, higher amounts of ABZs of at least 75% should be considered to ensure a sufficient increase in Shannon diversity and decrease in quasi-extinction risks. These high amounts of ABZs represent effective conservation measures to safeguard the stability of pollination services provided by solitary bee species. As the model structure can be easily adapted to other mobile species in agricultural landscapes, our community approach offers the chance to compare the effectiveness of conservation measures also for other pollinator communities in future.
KW  - agricultural landscape
KW  - buffer zones
KW  - community model
KW  - functional traits
KW  - solitary bees
KW  - spatially explicit
Y1  - 2022
U6  - https://doi.org/10.1002/ece3.8748
SN  - 2045-7758
VL  - 12
SP  - 1
EP  - 17
PB  - Wiley Online Library
CY  - Hoboken, New Jersey, USA
ET  - 3
ER  - 
TY  - JOUR
A1  - Kaunath, Vera
A1  - Eccard, Jana
T1  - Light Attraction in Carabid Beetles
BT  - Comparison Among Animals From the Inner City and a Dark Sky Reserve
JF  - Frontiers in Ecology and Evolution
N2  - Artificial light at night (ALAN) is altering the behaviour of nocturnal animals in a manifold of ways. Nocturnal invertebrates are particularly affected, due to their fatal attraction to ALAN. This selective pressure has the potential to reduce the strength of the flight-to-light response in insects, as shown recently in a moth species. Here we investigated light attraction of ground beetles (Coleoptera: Carabidae).We compared among animals (three genera) from a highly light polluted (HLP) grassland in the centre of Berlin and animals collected at a low-polluted area in a Dark Sky Reserve (DSR), captured using odour bait. In an arena setting tested at night time, HLP beetles (n = 75 across all genera) showed a reduced attraction towards ALAN. Tested during daytime, HLP beetles were less active in an open field test (measured as latency to start moving), compared to DSR (n = 143). However, we did not observe a reduced attraction towards ALAN within the species most common at both sides, Calathus fuscipes (HLP = 37, DSR = 118 individuals) indicating that not all species may be equally affected by ALAN. Reduced attraction to ALAN in urban beetles may either be a result of phenotypic selection in each generation removing HLP individuals that are attracted to light, or an indication for ongoing evolutionary differentiation among city and rural populations in their light response. Reduced attraction to light sources may directly enhance survival and reproductive success of urban individuals. However, decrease in mobility may negatively influence dispersal, reproduction and foraging success, highlighting the selective pressure that light pollution may have on fitness, by shaping and modifying the behaviour of insects.
KW  - light pollution
KW  - artificial light at night (ALAN)
KW  - Carabidae beetles
KW  - environmental change
KW  - Illuminance
KW  - solar powered light-emitting diode
Y1  - 2022
U6  - https://doi.org/10.3389/fevo.2022.751288
SN  - 2296-701X
N1  - VK and JE designed the experimental set up and research question. VK performed the animal trapping, experiments and hence, data collection, and organizing of the database. Both authors performed the statistical analyses and contributed to discussion, manuscript revision, read, and approved the submitted version.
VL  - 10
PB  - Frontiers Media
CY  - Lausanne, Schweiz
ER  - 
TY  - JOUR
A1  - Otto, Nils
A1  - Marelja, Zvonimir
A1  - Schoofs, Andreas
A1  - Kranenburg, Holger
A1  - Bittern, Jonas
A1  - Yildirim, Kerem
A1  - Berh, Dimitri
A1  - Bethke, Maria
A1  - Thomas, Silke
A1  - Rode, Sandra
A1  - Risse, Benjamin
A1  - Jiang, Xiaoyi
A1  - Pankratz, Michael
A1  - Leimkühler, Silke
A1  - Klämbt, Christian
T1  - The sulfite oxidase Shopper controls neuronal activity by regulating glutamate homeostasis in Drosophila ensheathing glia
JF  - Nature Communications
N2  - Specialized glial subtypes provide support to developing and functioning neural networks. Astrocytes modulate information processing by neurotransmitter recycling and release of neuromodulatory substances, whereas ensheathing glial cells have not been associated with neuromodulatory functions yet. To decipher a possible role of ensheathing glia in neuronal information processing, we screened for glial genes required in the Drosophila central nervous system for normal locomotor behavior. Shopper encodes a mitochondrial sulfite oxidase that is specifically required in ensheathing glia to regulate head bending and peristalsis. shopper mutants show elevated sulfite levels affecting the glutamate homeostasis which then act on neuronal network function. Interestingly, human patients lacking the Shopper homolog SUOX develop neurological symptoms, including seizures. Given an enhanced expression of SUOX by oligodendrocytes, our findings might indicate that in both invertebrates and vertebrates more than one glial cell type may be involved in modulating neuronal activity.
Y1  - 2018
U6  - https://doi.org/10.1038/s41467-018-05645-z
SN  - 2041-1723
VL  - 9
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Biterova, Ekaterina
A1  - Esmaeeli Moghaddam Tabalvandani, Mariam
A1  - Alanen, Heli I.
A1  - Saaranen, Mirva
A1  - Ruddock, Lloyd W.
T1  - Structures of Angptl3 and Angptl4, modulators of triglyceride levels and coronary artery disease
JF  - Scientific reports
N2  - Coronary artery disease is the most common cause of death globally and is linked to a number of risk factors including serum low density lipoprotein, high density lipoprotein, triglycerides and lipoprotein(a). Recently two proteins, angiopoietin-like protein 3 and 4, have emerged from genetic studies as being factors that significantly modulate plasma triglyceride levels and coronary artery disease. The exact function and mechanism of action of both proteins remains to be elucidated, however, mutations in these proteins results in up to 34% reduction in coronary artery disease and inhibition of function results in reduced plasma triglyceride levels. Here we report the crystal structures of the fibrinogen-like domains of both proteins. These structures offer new insights into the reported loss of function mutations, the mechanisms of action of the proteins and open up the possibility for the rational design of low molecular weight inhibitors for intervention in coronary artery disease.
Y1  - 2018
U6  - https://doi.org/10.1038/s41598-018-25237-7
SN  - 2045-2322
VL  - 8
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Wolff, Martin
A1  - Gast, Klaus
A1  - Evers, Andreas
A1  - Kurz, Michael
A1  - Pfeiffer-Marek, Stefania
A1  - Schüler, Anja
A1  - Seckler, Robert
A1  - Thalhammer, Anja
T1  - A Conserved Hydrophobic Moiety and Helix-Helix Interactions Drive the Self-Assembly of the Incretin Analog Exendin-4
JF  - Biomolecules
N2  - Exendin-4 is a pharmaceutical peptide used in the control of insulin secretion. Structural information on exendin-4 and related peptides especially on the level of quaternary structure is scarce. We present the first published association equilibria of exendin-4 directly measured by static and dynamic light scattering. We show that exendin-4 oligomerization is pH dependent and that these oligomers are of low compactness. We relate our experimental results to a structural hypothesis to describe molecular details of exendin-4 oligomers. Discussion of the validity of this hypothesis is based on NMR, circular dichroism and fluorescence spectroscopy, and light scattering data on exendin-4 and a set of exendin-4 derived peptides. The essential forces driving oligomerization of exendin-4 are helix–helix interactions and interactions of a conserved hydrophobic moiety. Our structural hypothesis suggests that key interactions of exendin-4 monomers in the experimentally supported trimer take place between a defined helical segment and a hydrophobic triangle constituted by the Phe22 residues of the three monomeric subunits. Our data rationalize that Val19 might function as an anchor in the N-terminus of the interacting helix-region and that Trp25 is partially shielded in the oligomer by C-terminal amino acids of the same monomer. Our structural hypothesis suggests that the Trp25 residues do not interact with each other, but with C-terminal Pro residues of their own monomers.
KW  - biophysics
KW  - diabetes
KW  - peptides
KW  - oligomerization
KW  - conformational change
KW  - molecular modeling
KW  - static and dynamic light scattering
KW  - spectroscopy
Y1  - 2021
U6  - https://doi.org/10.3390/biom11091305
SN  - 2218-273X
VL  - 11
IS  - 9
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Dunsing, Valentin
A1  - Luckner, Madlen
A1  - Zuehlke, Boris
A1  - Petazzi, Roberto Arturo
A1  - Herrmann, Andreas
A1  - Chiantia, Salvatore
T1  - Optimal fluorescent protein tags for quantifying protein oligomerization in living cells
JF  - Scientific reports
N2  - Fluorescence fluctuation spectroscopy has become a popular toolbox for non-disruptive analysis of molecular interactions in living cells. The quantification of protein oligomerization in the native cellular environment is highly relevant for a detailed understanding of complex biological processes. An important parameter in this context is the molecular brightness, which serves as a direct measure of oligomerization and can be easily extracted from temporal or spatial fluorescence fluctuations. However, fluorescent proteins (FPs) typically used in such studies suffer from complex photophysical transitions and limited maturation, inducing non-fluorescent states. Here, we show how these processes strongly affect molecular brightness measurements. We perform a systematic characterization of non-fluorescent states for commonly used FPs and provide a simple guideline for accurate, unbiased oligomerization measurements in living cells. Further, we focus on novel red FPs and demonstrate that mCherry2, an mCherry variant, possesses superior properties with regards to precise quantification of oligomerization.
Y1  - 2018
U6  - https://doi.org/10.1038/s41598-018-28858-0
SN  - 2045-2322
VL  - 8
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Zhang, Youjun
A1  - Chen, Moxian
A1  - Siemiatkowska, Beata
A1  - Toleco, Mitchell Rey
A1  - Jing, Yue
A1  - Strotmann, Vivien
A1  - Zhang, Jianghua
A1  - Stahl, Yvonne
A1  - Fernie, Alisdair R.
T1  - A highly efficient agrobacterium-mediated method for transient gene expression and functional studies in multiple plant species
JF  - Plant Communications
N2  - Although the use of stable transformation technology has led to great insight into gene function, its application in high-throughput studies remains arduous. Agro-infiltration have been widely used in species such as Nicotiana benthamiana for the rapid detection of gene expression and protein interaction analysis, but this technique does not work efficiently in other plant species, including Arabidopsis thaliana. As an efficient high-throughput transient expression system is currently lacking in the model plant species A. thaliana, we developed a method that is characterized by high efficiency, reproducibility, and suitability for transient expression of a variety of functional proteins in A. thaliana and 7 other plant species, including Brassica oleracea, Capsella rubella, Thellungiella salsuginea, Thellungiella halophila, Solanum tuberosum, Capsicum annuum, and N. benthamiana. Efficiency of this method was independently verified in three independent research facilities, pointing to the robustness of this technique. Furthermore, in addition to demonstrating the utility of this technique in a range of species, we also present a case study employing this method to assess protein-protein interactions in the sucrose biosynthesis pathway in Arabidopsis.
KW  - transient expression
KW  - agro-infiltration
KW  - subcellular localization
KW  - protein-protein interaction
Y1  - 2019
SN  - 2590-3462
VL  - 1
IS  - 5
PB  - Science Direct
CY  - New York
ER  - 
TY  - JOUR
A1  - Zwickel, Theresa
A1  - Kahl, Sandra M.
A1  - Rychlik, Michael
A1  - Müller, Marina E. H.
T1  - Chemotaxonomy of Mycotoxigenic Small-Spored Alternaria Fungi
BT  - Do Multitoxin Mixtures Act as an Indicator for Species Differentiation?
JF  - Frontiers in microbiology
N2  - Necrotrophic as well as saprophytic small-spored Altemaria (A.) species are annually responsible for major losses of agricultural products, such as cereal crops, associated with the contamination of food and feedstuff with potential health-endangering Altemaria toxins. Knowledge of the metabolic capabilities of different species-groups to form mycotoxins is of importance for a reliable risk assessment. 93 Altemaria strains belonging to the four species groups Alternaria tenuissima, A. arborescens, A. altemata, and A. infectoria were isolated from winter wheat kernels harvested from fields in Germany and Russia and incubated under equal conditions. Chemical analysis by means of an HPLC-MS/MS multi-Alternaria-toxin-method showed that 95% of all strains were able to form at least one of the targeted 17 non-host specific Altemaria toxins. Simultaneous production of up to 15 (modified) Altemaria toxins by members of the A. tenuissima, A. arborescens, A. altemata species-groups and up to seven toxins by A. infectoria strains was demonstrated. Overall tenuazonic acid was the most extensively formed mycotoxin followed by alternariol and alternariol mono methylether, whereas altertoxin I was the most frequently detected toxin. Sulfoconjugated modifications of alternariol, alternariol mono methylether, altenuisol and altenuene were frequently determined. Unknown perylene quinone derivatives were additionally detected. Strains of the species-group A. infectoria could be segregated from strains of the other three species-groups due to significantly lower toxin levels and the specific production of infectopyrone. Apart from infectopyrone, alterperylenol was also frequently produced by 95% of the A. infectoria strains. Neither by the concentration nor by the composition of the targeted Altemaria toxins a differentiation between the species-groups A. altemata, A. tenuissima and A. arborescens was possible.
KW  - small-spored Alternaria fungi
KW  - Alternaria species-groups
KW  - Alternaria mycotoxins
KW  - chemotaxonomy
KW  - secondary metabolite profiling
KW  - LC-MS/MS
KW  - wheat
KW  - perylene quinone derivatives
Y1  - 2018
U6  - https://doi.org/10.3389/fmicb.2018.01368
SN  - 1664-302X
VL  - 9
PB  - Frontiers Research Foundation
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Heger, Tina
A1  - Nikles, Gabriele
A1  - Jacobs, Brooke S.
T1  - Differentiation in native as well as introduced ranges
BT  - germination reflects mean and variance in cover of surrounding vegetation
JF  - AoB PLANTS
N2  - Germination, a crucial phase in the life cycle of a plant, can be significantly influenced by competition and facilitation. The aim of this study was to test whether differences in cover of surrounding vegetation can lead to population differentiation in germination behaviour of an annual grassland species, and if so, whether such a differentiation can be found in the native as well as in the introduced range. We used maternal progeny of Erodium cicutarium previously propagated under uniform conditions that had been collected in multiple populations in the native and two introduced ranges, in populations representing extremes in terms of mean and variability of the cover of surrounding vegetation. In the first experiment, we tested the effect of germination temperature and mean cover at the source site on germination, and found interlinked effects of these factors. In seeds from one of the introduced ranges (California), we found indication for a 2-fold dormancy, hindering germination at high temperatures even if physical dormancy was broken and water was available. This behaviour was less strong in high cover populations, indicating cross-generational facilitating effects of dense vegetation. In the second experiment, we tested whether spatial variation in cover of surrounding vegetation has an effect on the proportion of dormant seeds. Contrary to our expectations, we found that across source regions, high variance in cover was associated with higher proportions of seeds germinating directly after storage. In all three regions, germination seemed to match the local environment in terms of climate and vegetation cover. We suggest that this is due to a combined effect of introduction of preadapted genotypes and local evolutionary processes.
KW  - Bet-hedging
KW  - competition
KW  - eco-evolutionary experience
KW  - facilitation
KW  - genetic adaptation
KW  - physical and physiological dormancy
KW  - preadaptation
Y1  - 2018
U6  - https://doi.org/10.1093/aobpla/ply009
SN  - 2041-2851
VL  - 10
IS  - 1
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Käch, Heidi
A1  - Mathe-Hubert, Hugo
A1  - Dennis, Alice B.
A1  - Vorburger, Christoph
T1  - Rapid evolution of symbiont-mediated resistance compromises biological control of aphids by parasitoids
JF  - Evolutionary applications
N2  - There is growing interest in biological control as a sustainable and environmentally friendly way to control pest insects. Aphids are among the most detrimental agricultural pests worldwide, and parasitoid wasps are frequently employed for their control. The use of asexual parasitoids may improve the effectiveness of biological control because only females kill hosts and because asexual populations have a higher growth rate than sexuals. However, asexuals may have a reduced capacity to track evolutionary change in their host populations. We used a factorial experiment to compare the ability of sexual and asexual populations of the parasitoid Lysiphlebus fabarum to control caged populations of black bean aphids (Aphis fabae) of high and low clonal diversity. The aphids came from a natural population, and one-third of the aphid clones harbored Hamiltonella defensa, a heritable bacterial endosymbiont that increases resistance to parasitoids. We followed aphid and parasitoid population dynamics for 3months but found no evidence that the reproductive mode of parasitoids affected their effectiveness as biocontrol agents, independent of host clonal diversity. Parasitoids failed to control aphids in most cases, because their introduction resulted in strong selection for clones protected by H.defensa. The increasingly resistant aphid populations escaped control by parasitoids, and we even observed parasitoid extinctions in many cages. The rapid evolution of symbiont-conferred resistance in turn imposed selection on parasitoids. In cages where asexual parasitoids persisted until the end of the experiment, they became dominated by a single genotype able to overcome the protection provided by H.defensa. Thus, there was evidence for parasitoid counteradaptation, but it was generally too slow for parasitoids to regain control over aphid populations. It appears that when pest aphids possess defensive symbionts, the presence of parasitoid genotypes able to overcome symbiont-conferred resistance is more important for biocontrol success than their reproductive mode.
KW  - aphids
KW  - Aphis fabae
KW  - biological control
KW  - defensive symbiosis
KW  - Hamiltonella defensa
KW  - Lysiphlebus fabarum
KW  - parasitoid
KW  - resistance
Y1  - 2018
U6  - https://doi.org/10.1111/eva.12532
SN  - 1752-4571
VL  - 11
IS  - 2
SP  - 220
EP  - 230
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Shi, Jun
A1  - Joshi, Jasmin Radha
A1  - Tielboerger, Katja
A1  - Verhoeven, Koen J. F.
A1  - Macel, Mirka
T1  - Costs and benefits of admixture between foreign genotypes and local populations in the field
JF  - Ecology and evolution
N2  - Admixture is the hybridization between populations within one species. It can increase plant fitness and population viability by alleviating inbreeding depression and increasing genetic diversity. However, populations are often adapted to their local environments and admixture with distant populations could break down local adaptation by diluting the locally adapted genomes. Thus, admixed genotypes might be selected against and be outcompeted by locally adapted genotypes in the local environments. To investigate the costs and benefits of admixture, we compared the performance of admixed and within-population F1 and F2 generations of the European plant Lythrum salicaria in a reciprocal transplant experiment at three European field sites over a 2-year period. Despite strong differences between site and plant populations for most of the measured traits, including herbivory, we found limited evidence for local adaptation. The effects of admixture depended on experimental site and plant population, and were positive for some traits. Plant growth and fruit production of some populations increased in admixed offspring and this was strongest with larger parental distances. These effects were only detected in two of our three sites. Our results show that, in the absence of local adaptation, admixture may boost plant performance, and that this is particularly apparent in stressful environments. We suggest that admixture between foreign and local genotypes can potentially be considered in nature conservation to restore populations and/or increase population viability, especially in small inbred or maladapted populations.
KW  - heterosis
KW  - inbreeding depression
KW  - local adaptation
KW  - Lythrum salicaria
KW  - outbreeding depression
Y1  - 2018
U6  - https://doi.org/10.1002/ece3.3946
SN  - 2045-7758
VL  - 8
IS  - 7
SP  - 3675
EP  - 3684
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Weithoff, Guntram
A1  - Taube, Anne
A1  - Bolius, Sarah
T1  - The invasion success of the cyanobacterium Cylindrospermopsis raciborskii in experimental mesocosms
BT  - genetic identity, grazing loss, competition and biotic resistance
JF  - Aquatic Invasions
N2  - The potentially toxic, invasive cyanobacterium Cylindrospermopsis raciborskii, originating from sub-tropical regions, has spread into temperate climate zones in almost all continents. Potential factors in its success are temperature, light and nutrient levels. Grazing losses through zooplankton have been measured in the laboratory but are typically not regarded as a factor in (failed) invasion success. In some potentially suitable lakes, C. raciborskii has never been found, although it is present in water bodies close by. Therefore, we tested the invasive potential of three different isolates introduced into natural plankton communities using laboratory mesocosm experiments under three grazing levels: ambient zooplankton densities, removal of large species using 100 mu m mesh and a ca. doubling of large species. Three C. raciborskii isolates originating from the same geographic region (North-East Germany) were added separately to the four replicates of each treatment and kept in semi-continuous cultures for 21 days. Two isolates disappeared from the mesocosms and were also not viable in filtered lake water indicating that the lake water itself or the switch from culture medium to lake water led to the decay of the inoculated C. raciborskii. Only one out of the three isolates persisted in the plankton communities at a rather low level and only in the treatment without larger zooplankton. This result demonstrates that under potentially suitable environmental conditions, top-down control from zooplankton might hamper the establishment of C. raciborskii. Non-metric multidimensional scaling showed distinct variation in resident phytoplankton communities between the different grazing levels, thus differential grazing impact shaped the resident community in different ways allowing C. raciborskii only to invade under competitive (= low grazing pressure) conditions. Furthermore, even after invasion failure, the temporary presence of C. raciborskii influenced the phytoplankton community.
KW  - alien species
KW  - Cyanobacteria
KW  - competitive resistance
KW  - consumptive resistance
KW  - herbivory
KW  - harmful algae
KW  - microbial invasion
Y1  - 2017
U6  - https://doi.org/10.3391/ai.2017.12.3.07
SN  - 1798-6540
SN  - 1818-5487
VL  - 12
SP  - 333
EP  - 341
PB  - Regional Euro-Asian Biological Invasions centre-reabic
CY  - Helsinki
ER  - 
TY  - JOUR
A1  - Martins, Renata F.
A1  - Schmidt, Anke
A1  - Lenz, Dorina
A1  - Wilting, Andreas
A1  - Fickel, Jörns
T1  - Historical biogeography of Rusa unicolor and R-timorensis
BT  - Historical biogeography of Rusa unicolor and R. timorensis
JF  - Ecology and evolution
N2  - In this study we compared the phylogeographic patterns of two Rusa species, Rusa unicolor and Rusa timorensis, in order to understand what drove and maintained differentiation between these two geographically and genetically close species and investigated the route of introduction of individuals to the islands outside of the Sunda Shelf. We analyzed full mitogenomes from 56 archival samples from the distribution areas of the two species and 18 microsatellite loci in a subset of 16 individuals to generate the phylogeographic patterns of both species. Bayesian inference with fossil calibration was used to estimate the age of each species and major divergence events. Our results indicated that the split between the two species took place during the Pleistocene, similar to 1.8Mya, possibly driven by adaptations of R. timorensis to the drier climate found on Java compared to the other islands of Sundaland. Although both markers identified two well-differentiated clades, there was a largely discrepant pattern between mitochondrial and nuclear markers. While nDNA separated the individuals into the two species, largely in agreement with their museum label, mtDNA revealed that all R. timorensis sampled to the east of the Sunda shelf carried haplotypes from R. unicolor and one Rusa unicolor from South Sumatra carried a R. timorensis haplotype. Our results show that hybridization occurred between these two sister species in Sundaland during the Late Pleistocene and resulted in human-mediated introduction of hybrid descendants in all islands outside Sundaland.
KW  - Cervidae
KW  - human introduction
KW  - hybridization
KW  - Phylogeography
KW  - Sundaland
Y1  - 2017
U6  - https://doi.org/10.1002/ece3.3754
SN  - 2045-7758
VL  - 8
IS  - 3
SP  - 1465
EP  - 1479
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Bukowski, Alexandra R.
A1  - Schittko, Conrad
A1  - Petermann, Jana S.
T1  - The strength of negative plant-soil feedback increases from the intraspecific to the interspecific and the functional group level
JF  - Ecology and evolution
N2  - One of the processes that may play a key role in plant species coexistence and ecosystem functioning is plant-soil feedback, the effect of plants on associated soil communities and the resulting feedback on plant performance. Plant-soil feedback at the interspecific level (comparing growth on own soil with growth on soil from different species) has been studied extensively, while plant-soil feedback at the intraspecific level (comparing growth on own soil with growth on soil from different accessions within a species) has only recently gained attention. Very few studies have investigated the direction and strength of feedback among different taxonomic levels, and initial results have been inconclusive, discussing phylogeny, and morphology as possible determinants. To test our hypotheses that the strength of negative feedback on plant performance increases with increasing taxonomic level and that this relationship is explained by morphological similarities, we conducted a greenhouse experiment using species assigned to three taxonomic levels (intraspecific, interspecific, and functional group level). We measured certain fitness-related aboveground traits and used them along literature-derived traits to determine the influence of morphological similarities on the strength and direction of the feedback. We found that the average strength of negative feedback increased from the intraspecific over the interspecific to the functional group level. However, individual accessions and species differed in the direction and strength of the feedback. None of our results could be explained by morphological dissimilarities or individual traits. Synthesis. Our results indicate that negative plant-soil feedback is stronger if the involved plants belong to more distantly related species. We conclude that the taxonomic level is an important factor in the maintenance of plant coexistence with plant-soil feedback as a potential stabilizing mechanism and should be addressed explicitly in coexistence research, while the traits considered here seem to play a minor role.
KW  - Arabidopsis thaliana Col-0
KW  - home-away effect
KW  - intraspecific diversity
KW  - morphological similarities
KW  - dissimilarities of plants
KW  - plant-soil (belowground) interactions
KW  - species coexistence
KW  - taxonomic levels
KW  - trait measurements
Y1  - 2018
U6  - https://doi.org/10.1002/ece3.3755
SN  - 2045-7758
VL  - 8
IS  - 4
SP  - 2280
EP  - 2289
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Küçükgöze, Gökhan
A1  - Leimkühler, Silke
T1  - Direct comparison of the four aldehyde oxidase enzymes present in mouse gives insight into their substrate specificities
JF  - PLOS ONE
N2  - Mammalian aldehyde oxidases (AOXs) are molybdo-flavoenzymes which are present in many tissues in various mammalian species, including humans and rodents. Different species contain a different number of AOX isoforms. In particular, the reasons why mammals other than humans express a multiplicity of tissue-specific AOX enzymes is unknown. In mouse, the isoforms mAOX1, mAOX3, mAOX4 and mAOX2 are present. We previously established a codon-optimized heterologous expression systems for the mAOX1-4 isoforms in Escherichia coli that gives yield to sufficient amounts of active protein for kinetic characterizations and sets the basis in this study for site-directed mutagenesis and structure-function studies. A direct and simultaneous comparison of the enzymatic properties and characteristics of the four enzymes on a larger number of substrates has never been performed. Here, thirty different structurally related aromatic, aliphatic and N-heterocyclic compounds were used as substrates, and the kinetic parameters of all four mAOX enzymes were directly compared. The results show that especially mAOX4 displays a higher substrate selectivity, while no major differences between mAOX1, mAOX2 and mAOX3 were identified. Generally, mAOX1 was the enzyme with the highest catalytic turnover for most substrates. To understand the factors that contribute to the substrate specificity of mAOX4, site-directed mutagenesis was applied to substitute amino acids in the substrate-binding funnel by the ones present in mAOX1, mAOX3, and mAOX2. An increase in activity was obtained by the amino acid exchange M1088V in the active site identified to be specific for mAOX4, to the amino acid identified in mAOX3.
Y1  - 2018
U6  - https://doi.org/10.1371/journal.pone.0191819
SN  - 1932-6203
VL  - 13
IS  - 1
PB  - Public Library of Science
CY  - San Fransisco
ER  - 
TY  - JOUR
A1  - Tiedemann, Kim
A1  - Iobbi-Nivol, Chantal
A1  - Leimkühler, Silke
T1  - The Role of the Nucleotides in the Insertion of the bis-Molybdopterin Guanine Dinucleotide Cofactor into apo-Molybdoenzymes
JF  - Molecules
N2  - The role of the GMP nucleotides of the bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor of the DMSO reductase family has long been a subject of discussion. The recent characterization of the bis-molybdopterin (bis-Mo-MPT) cofactor present in the E. coli YdhV protein, which differs from bis-MGD solely by the absence of the nucleotides, now enables studying the role of the nucleotides of bis-MGD and bis-MPT cofactors in Moco insertion and the activity of molybdoenzymes in direct comparison. Using the well-known E. coli TMAO reductase TorA as a model enzyme for cofactor insertion, we were able to show that the GMP nucleotides of bis-MGD are crucial for the insertion of the bis-MGD cofactor into apo-TorA.
KW  - bis-MGD
KW  - chaperone
KW  - molybdenum cofactor
KW  - TMAO reductase
Y1  - 2022
U6  - https://doi.org/10.3390/molecules27092993
SN  - 1420-3049
VL  - 27
SP  - 1
EP  - 15
PB  - MDPI
CY  - Basel, Schweiz
ET  - 9
ER  - 
TY  - JOUR
A1  - Yarman, Aysu
A1  - Scheller, Frieder W.
T1  - How reliable is the electrochemical readout of MIP sensors?
JF  - Sensors
N2  - Electrochemical methods offer the simple characterization of the synthesis of molecularly imprinted polymers (MIPs) and the readouts of target binding. The binding of electroinactive analytes can be detected indirectly by their modulating effect on the diffusional permeability of a redox marker through thin MIP films. However, this process generates an overall signal, which may include nonspecific interactions with the nonimprinted surface and adsorption at the electrode surface in addition to (specific) binding to the cavities. Redox-active low-molecular-weight targets and metalloproteins enable a more specific direct quantification of their binding to MIPs by measuring the faradaic current. The in situ characterization of enzymes, MIP-based mimics of redox enzymes or enzyme-labeled targets, is based on the indication of an electroactive product. This approach allows the determination of both the activity of the bio(mimetic) catalyst and of the substrate concentration.
KW  - molecularly imprinted polymers
KW  - electropolymerization
KW  - direct electron
KW  - transfer
KW  - catalysis
KW  - redox marker
KW  - gate effect
Y1  - 2020
U6  - https://doi.org/10.3390/s20092677
SN  - 1424-8220
VL  - 20
IS  - 9
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Weithoff, Guntram
A1  - Bell, Elanor Margaret
T1  - Complex Trophic Interactions in an Acidophilic Microbial Community
JF  - Microorganisms
N2  - Extreme habitats often harbor specific communities that differ substantially from non-extreme habitats. In many cases, these communities are characterized by archaea, bacteria and protists, whereas the number of species of metazoa and higher plants is relatively low. In extremely acidic habitats, mostly prokaryotes and protists thrive, and only very few metazoa thrive, for example, rotifers. Since many studies have investigated the physiology and ecology of individual species, there is still a gap in research on direct, trophic interactions among extremophiles. To fill this gap, we experimentally studied the trophic interactions between a predatory protist (Actinophrys sol, Heliozoa) and its prey, the rotifers Elosa woralli and Cephalodella sp., the ciliate Urosomoida sp. and the mixotrophic protist Chlamydomonas acidophila (a green phytoflagellate, Chlorophyta). We found substantial predation pressure on all animal prey. High densities of Chlamydomonas acidophila reduced the predation impact on the rotifers by interfering with the feeding behaviour of A. sol. These trophic relations represent a natural case of intraguild predation, with Chlamydomonas acidophila being the common prey and the rotifers/ciliate and A. sol being the intraguild prey and predator, respectively. We further studied this intraguild predation along a resource gradient using Cephalodella sp. as the intraguild prey. The interactions among the three species led to an increase in relative rotifer abundance with increasing resource (Chlamydomonas) densities. By applying a series of laboratory experiments, we revealed the complexity of trophic interactions within a natural extremophilic community.
KW  - acid mine drainage
KW  - extremophiles
KW  - food web
KW  - heliozoa
KW  - intraguild predation
KW  - mining lakes
KW  - Rotifera
Y1  - 2022
U6  - https://doi.org/10.3390/microorganisms10071340
SN  - 2076-2607
VL  - 10
SP  - 1
EP  - 10
PB  - MDPI
CY  - Basel, Schweiz
ET  - 7
ER  - 
TY  - JOUR
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
JF  - Biosensors
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.
KW  - redox polymer
KW  - aldehyde oxidoreductase
KW  - ionic strength
KW  - benzaldehyde
KW  - GABA
KW  - biosensor
Y1  - 2014
U6  - https://doi.org/10.3390/bios4040403
VL  - 4
IS  - 4
SP  - 403
EP  - 421
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Mitic, Kristina
A1  - Grafe, Marianne
A1  - Batsios, Petros
A1  - Meyer, Irene
T1  - Partial Disassembly of the Nuclear Pore Complex Proteins during Semi-Closed Mitosis in Dictyostelium discoideum
JF  - Cells
N2  - Dictyostelium cells undergo a semi-closed mitosis, during which the nuclear envelope (NE) persists; however, free diffusion between the cytoplasm and the nucleus takes place. To permit the formation of the mitotic spindle, the nuclear envelope must be permeabilized in order to allow diffusion of tubulin dimers and spindle assembly factors into the nucleus. In Aspergillus, free diffusion of proteins between the cytoplasm and the nucleus is achieved by a partial disassembly of the nuclear pore complexes (NPCs) prior to spindle assembly. In order to determine whether this is also the case in Dictyostelium, we analysed components of the NPC by immunofluorescence microscopy and live cell imaging and studied their behaviour during interphase and mitosis. We observed that the NPCs are absent from the contact area of the nucleoli and that some nucleoporins also localize to the centrosome and the spindle poles. In addition, we could show that, during mitosis, the central FG protein NUP62, two inner ring components and Gle1 depart from the NPCs, while all other tested NUPs remained at the NE. This leads to the conclusion that indeed a partial disassembly of the NPCs takes place, which contributes to permeabilisation of the NE during semi-closed mitosis.
KW  - nuclear pore complex
KW  - nucleoporins
KW  - semi-closed mitosis
KW  - centrosome
KW  - Dictyostelium
Y1  - 2021
U6  - https://doi.org/10.3390/cells11030407
SN  - 2073-4409
VL  - 11
IS  - 3
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Grafe, Marianne
A1  - Hofmann, Phillip
A1  - Batsios, Petros
A1  - Meyer, Irene
A1  - Gräf, Ralph
T1  - In vivo assembly of a Dictyostelium lamin mutant induced by light, mechanical stress, and pH
JF  - Cells : open access journal
N2  - We expressedDictyosteliumlamin (NE81) lacking both a functional nuclear localization signal and a CAAX-box for C-terminal lipid modification. This lamin mutant assembled into supramolecular, three-dimensional clusters in the cytosol that disassembled at the onset of mitosis and re-assembled in late telophase, thus mimicking the behavior of the endogenous protein. As disassembly is regulated by CDK1-mediated phosphorylation at serine 122, we generated a phosphomimetic S122E mutant called GFP-NE81-S122E-Delta NLS Delta CLIM. Surprisingly, during imaging, the fusion protein assembled into cytosolic clusters, similar to the protein lacking the phosphomimetic mutation. Clusters disassembled again in the darkness. Assembly could be induced with blue but not green or near ultraviolet light, and it was independent of the fusion tag. Assembly similarly occurred upon cell flattening. Earlier reports and own observations suggested that both blue light and cell flattening could result in a decrease of intracellular pH. Indeed, keeping the cells at low pH also reversibly induced cluster formation. Our results indicate that lamin assembly can be induced by various stress factors and that these are transduced via intracellular acidification. Although these effects have been shown in a phosphomimetic CDK1 mutant of theDictyosteliumlamin, they are likely relevant also for wild-type lamin.
KW  - lamin
KW  - NE81
KW  - Dictyostelium
KW  - nuclear envelope
KW  - nuclear lamina
Y1  - 2020
U6  - https://doi.org/10.3390/cells9081834
SN  - 2073-4409
VL  - 9
IS  - 8
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Neumann, Bettina
A1  - Wollenberger, Ulla
T1  - Electrochemical biosensors employing natural and artificial heme peroxidases on semiconductors
JF  - Sensors
N2  - Heme peroxidases are widely used as biological recognition elements in electrochemical biosensors for hydrogen peroxide and phenolic compounds. Various nature-derived and fully synthetic heme peroxidase mimics have been designed and their potential for replacing the natural enzymes in biosensors has been investigated. The use of semiconducting materials as transducers can thereby offer new opportunities with respect to catalyst immobilization, reaction stimulation, or read-out. This review focuses on approaches for the construction of electrochemical biosensors employing natural heme peroxidases as well as various mimics immobilized on semiconducting electrode surfaces. It will outline important advances made so far as well as the novel applications resulting thereof.
KW  - electrochemical biosensors
KW  - heme
KW  - peroxidases
KW  - semiconductors
KW  - peroxidase mimics
Y1  - 2020
U6  - https://doi.org/10.3390/s20133692
SN  - 1424-8220
VL  - 20
IS  - 13
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Müller, Marik
A1  - Nedielkov, Ruslan
A1  - Arndt, Katja M.
T1  - Strategies for Enzymatic Inactivation of the Veterinary  Antibiotic Florfenicol
JF  - Antibiotics
N2  - Large quantities of the antibiotic florfenicol are used in animal farming and aquaculture, contaminating the ecosystem with antibiotic residues and promoting antimicrobial resistance, ultimately leading to untreatable multidrug-resistant pathogens. Florfenicol-resistant bacteria often activate export mechanisms that result in resistance to various structurally unrelated antibiotics. We devised novel strategies for the enzymatic inactivation of florfenicol in different media, such as saltwater or milk. Using a combinatorial approach and selection, we optimized a hydrolase (EstDL136) for florfenicol cleavage. Reaction kinetics were followed by time-resolved NMR spectroscopy. Importantly, the hydrolase remained active in different media, such as saltwater or cow milk. Various environmentally-friendly application strategies for florfenicol inactivation were developed using the optimized hydrolase. As a potential filter device for cost-effective treatment of waste milk or aquacultural wastewater, the hydrolase was immobilized on Ni-NTA agarose or silica as carrier materials. In two further application examples, the hydrolase was used as cell extract or encapsulated with a semi-permeable membrane. This facilitated, for example, florfenicol inactivation in whole milk, which can help to treat waste milk from medicated cows, to be fed to calves without the risk of inducing antibiotic resistance. Enzymatic inactivation of antibiotics, in general, enables therapeutic intervention without promoting antibiotic resistance.
KW  - aquaculture
KW  - antibiotic inactivation
KW  - enzyme optimization
KW  - enzymatic inactivation
KW  - florfenicol
KW  - immobilization
KW  - industrial farming
Y1  - 2022
U6  - https://doi.org/10.3390/antibiotics11040443
SN  - 2079-6382
VL  - 11
IS  - 4
SP  - 1
EP  - 18
PB  - MDPI
CY  - Basel, Schweiz
ER  - 
TY  - JOUR
A1  - Paraskevopoulou, Sofia
A1  - Dennis, Alice B.
A1  - Weithoff, Guntram
A1  - Tiedemann, Ralph
T1  - Temperature-dependent life history and transcriptomic responses in heat-tolerant versus heat-sensitive Brachionus rotifers
JF  - Scientific Reports
N2  - Thermal stress response is an essential physiological trait that determines occurrence and temporal succession in nature, including response to climate change. We compared temperature-related demography in closely related heat-tolerant and heat-sensitive Brachionus rotifer species. We found significant differences in heat response, with the heat-sensitive species adopting a strategy of long survival and low population growth, while the heat-tolerant followed the opposite strategy. In both species, we examined the genetic basis of physiological variation by comparing gene expression across increasing temperatures. Comparative transcriptomic analyses identified shared and opposing responses to heat. Interestingly, expression of heat shock proteins (hsps) was strikingly different in the two species and mirrored differences in population growth rates, showing that hsp genes are likely a key component of a species’ adaptation to different temperatures. Temperature induction caused opposing patterns of expression in further functional categories including energy, carbohydrate and lipid metabolism, and in genes related to ribosomal proteins. In the heat-sensitive species, elevated temperatures caused up-regulation of genes related to meiosis induction and post-translational histone modifications. This work demonstrates the sweeping reorganizations of biological functions that accompany temperature adaptation in these two species and reveals potential molecular mechanisms that might be activated for adaptation to global warming.
KW  - Ecology
KW  - Evolution
KW  - Oyster Crassostrea-gigas
KW  - cryptic species complex
KW  - pacific oyster
KW  - thermal-stress
KW  - genetic differentiation
KW  - expression patterns
KW  - molecular phylogeny
KW  - shock proteins
KW  - evolutionary
KW  - hsp70
Y1  - 2020
U6  - https://doi.org/10.1038/s41598-020-70173-0
SN  - 2045-2322
VL  - 10
PB  - Macmillan Publishers Limited, part of Springer Nature
CY  - London
ER  - 
TY  - JOUR
A1  - Romero-Mujalli, Daniel
A1  - Rochow, Markus
A1  - Kahl, Sandra M.
A1  - Paraskevopoulou, Sofia
A1  - Folkertsma, Remco
A1  - Jeltsch, Florian
A1  - Tiedemann, Ralph
T1  - Adaptive and nonadaptive plasticity in changing environments: Implications for sexual species with different life history strategies
JF  - Ecology and Evolution
N2  - Populations adapt to novel environmental conditions by genetic changes or phenotypic plasticity. Plastic responses are generally faster and can buffer fitness losses  under variable conditions. Plasticity is typically modeled as random noise and linear reaction norms that assume simple one-to- one  genotype–phenotype maps and no limits to the phenotypic response. Most studies on plasticity have focused on its effect on population viability. However, it is not clear, whether the advantage of plasticity depends solely on environmental fluctuations or also on the genetic and demographic properties (life histories) of populations. Here we present an individual-based model and study the relative importance of adaptive and nonadaptive plasticity for populations of sexual species with different life histories experiencing directional stochastic climate change. Environmental fluctuations were simulated using differentially autocorrelated climatic stochasticity or noise color, and scenarios of directiona
climate change. Nonadaptive plasticity was simulated as a random environmental effect on trait development, while adaptive plasticity as a linear, saturating, or sinusoidal reaction norm. The last two imposed limits to the plastic response and emphasized flexible interactions of the genotype with the environment. Interestingly, this assumption led to (a) smaller phenotypic than genotypic variance in the population (many-to- one genotype–phenotype map) and the coexistence of polymorphisms, and (b) the maintenance of higher genetic variation—compared to linear reaction norms and genetic determinism—even when the population was exposed to a constant environment for several generations. Limits to plasticity led to genetic accommodation, when costs were negligible, and to the appearance of cryptic variation when limits were exceeded. We found that adaptive plasticity promoted population persistence under red environmental noise and was particularly important for life histories with low fecundity. Populations produing more offspring could cope with environmental fluctuations solely by genetic changes or random plasticity, unless environmental change was too fast.
KW  - developmental canalization
KW  - environmental change
KW  - genetic accommodation
KW  - Individual-based models
KW  - limits
KW  - many-to-one genotype–phenotype map
KW  - noise color
KW  - phenotypic plasticity
KW  - reaction norms
KW  - stochastic fluctuations
Y1  - 2020
SN  - 2045-7758
VL  - 11
IS  - 11
PB  - John Wiley & Sons, Inc.
CY  - New Jersey
ER  - 
TY  - JOUR
A1  - Senczuk, Gabriele
A1  - Havenstein, Katja
A1  - Milana, Valentina
A1  - Ripa, Chiara
A1  - De Simone, Emanuela
A1  - Tiedemann, Ralph
A1  - Castiglia, Riccardo
T1  - Spotlight on islands
BT  - on the origin and diversification of an ancient lineage of the Italian wall lizard Podarcis siculus in the western Pontine Islands
JF  - Scientific reports
N2  - Groups of proximate continental islands may conceal more tangled phylogeographic patterns than oceanic archipelagos as a consequence of repeated sea level changes, which allow populations to experience gene flow during periods of low sea level stands and isolation by vicariant mechanisms during periods of high sea level stands. Here, we describe for the first time an ancient and diverging lineage of the Italian wall lizard Podarcis siculus from the western Pontine Islands. We used nuclear and mitochondrial DNA sequences of 156 individuals with the aim of unraveling their phylogenetic position, while microsatellite loci were used to test several a priori insular biogeographic models of migration with empirical data. Our results suggest that the western Pontine populations colonized the islands early during their Pliocene volcanic formation, while populations from the eastern Pontine Islands seem to have been introduced recently. The inter-island genetic makeup indicates an important role of historical migration, probably due to glacial land bridges connecting islands followed by a recent vicariant mechanism of isolation. Moreover, the most supported migration model predicted higher gene flow among islands which are geographically arranged in parallel. Considering the threatened status of small insular endemic populations, we suggest this new evolutionarily independent unit be given priority in conservation efforts.
Y1  - 2018
U6  - https://doi.org/10.1038/s41598-018-33326-w
SN  - 2045-2322
VL  - 8
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Cahsan, Binia De
A1  - Westbury, Michael V.
A1  - Paraskevopoulou, Sofia
A1  - Drews, Hauke
A1  - Ott, Moritz
A1  - Gollmann, Günter
A1  - Tiedemann, Ralph
T1  - Genomic consequences of human-mediated translocations in margin populations of an endangered amphibian
JF  - Evolutionary Applications
N2  - Due to their isolated and often fragmented nature, range margin populations are especially vulnerable to rapid environmental change. To maintain genetic diversity and adaptive potential, gene flow from disjunct populations might therefore be crucial to their survival. Translocations are often proposed as a mitigation strategy to increase genetic diversity in threatened populations. However, this also includes the risk of losing locally adapted alleles through genetic swamping. Human-mediated translocations of southern lineage specimens into northern German populations of the endangered European fire-bellied toad (Bombina bombina) provide an unexpected experimental set-up to test the genetic consequences of an intraspecific introgression from central population individuals into populations at the species range margin. Here, we utilize complete mitochondrial genomes and transcriptome nuclear data to reveal the full genetic extent of this translocation and the consequences it may have for these populations. We uncover signs of introgression in four out of the five northern populations investigated, including a number of introgressed alleles ubiquitous in all recipient populations, suggesting a possible adaptive advantage. Introgressed alleles dominate at the MTCH2 locus, associated with obesity/fat tissue in humans, and the DSP locus, essential for the proper development of epidermal skin in amphibians. Furthermore, we found loci where local alleles were retained in the introgressed populations, suggesting their relevance for local adaptation. Finally, comparisons of genetic diversity between introgressed and nonintrogressed northern German populations revealed an increase in genetic diversity in all German individuals belonging to introgressed populations, supporting the idea of a beneficial transfer of genetic variation from Austria into North Germany.
KW  - adaptive introgression
KW  - admixture
KW  - Bombina bombina
KW  - genetic rescue
KW  - mitogenomes
KW  - transcriptomics
Y1  - 2020
SN  - 1752-4563
VL  - 14
IS  - 6
PB  - John Wiley & Sons, Inc.
CY  - New Jersey
ER  - 
TY  - JOUR
A1  - Spikes, Montrai
A1  - Rodríguez-Silva, Rodet
A1  - Bennett, Kerri-Ann
A1  - Bräger, Stefan
A1  - Josaphat, James
A1  - Torres-Pineda, Patricia
A1  - Ernst, Anja
A1  - Havenstein, Katja
A1  - Schlupp, Ingo
A1  - Tiedemann, Ralph
T1  - A phylogeny of the genus Limia (Teleostei: Poeciliidae) suggests a single-lake radiation nested in a Caribbean-wide allopatric speciation scenario
JF  - BMC Research Notes
N2  - Objective
The Caribbean is an important global biodiversity hotspot. Adaptive radiations there lead to many speciation events within a limited period and hence are particularly prominent biodiversity generators. A prime example are freshwater fish of the genus Limia, endemic to the Greater Antilles. Within Hispaniola, nine species have been described from a single isolated site, Lake Miragoâne, pointing towards extraordinary sympatric speciation. This study examines the evolutionary history of the Limia species in Lake Miragoâne, relative to their congeners throughout the Caribbean.

Results
For 12 Limia species, we obtained almost complete sequences of the mitochondrial cytochrome b gene, a well-established marker for lower-level taxonomic relationships. We included sequences of six further Limia species from GenBank (total N  = 18 species). Our phylogenies are in concordance with other published phylogenies of Limia. There is strong support that the species found in Lake Miragoâne in Haiti are monophyletic, confirming a recent local radiation. Within Lake Miragoâne, speciation is likely extremely recent, leading to incomplete lineage sorting in the mtDNA. Future studies using multiple unlinked genetic markers are needed to disentangle the relationships within the Lake Miragoâne clade.
KW  - Cytochrome b
KW  - Island biogeography
KW  - Fresh water fish
KW  - Phylogeny
Y1  - 2021
U6  - https://doi.org/10.1186/s13104-021-05843-x
SN  - 1756-0500
VL  - 14
SP  - 1
EP  - 8
PB  - BMC Research Notes / Biomed Central
CY  - London
ER  - 
TY  - JOUR
A1  - Gross, Stephanie
A1  - Claus, Philip
A1  - Wohlsein, Peter
A1  - Kesselring, Tina
A1  - Lakemeyer, Jan
A1  - Reckendorf, Anja
A1  - Roller, Marco
A1  - Tiedemann, Ralph
A1  - Siebert, Ursula
T1  - Indication of lethal interactions between a solitary bottlenose dolphin (Tursiops truncatus) and harbor porpoises (Phocoena phocoena) in the German Baltic Sea
JF  - BMC zoology
N2  - Background Aggressive interactions between bottlenose dolphins (Tursiops truncatus) and harbor porpoises (Phocoena phocoena) have been reported in different parts of the world since the late 1990s. In the Baltic Sea, harbor porpoises are the only native cetacean species, while bottlenose dolphins may appear there temporarily. In the fall of 2016, a solitary male photo-identified bottlenose dolphin stayed in the German Baltic Sea of Schleswig-Holstein for 3 months. During that time, the necropsies of the stranded harbor porpoises revealed types of trauma of varying degrees in six animals, which is unusual in this area. The purpose of this study was to determine if the appearance of the bottlenose dolphin could be linked to the trauma of the harbor porpoise carcasses. Results Pathological findings in these animals included subcutaneous, thoracic and abdominal hemorrhages, multiple, mainly bilateral, rib fractures, and one instance of lung laceration. These findings correspond with the previously reported dolphin-caused injuries in other regions. Moreover, public sighting reports showed a spatial and temporal correlation between the appearance of the dolphin and the stranding of fatally injured harbor porpoises. Conclusion Despite the fact that no attack has been witnessed in German waters to date, our findings indicate the first record of lethal interactions between a bottlenose dolphin and harbor porpoises in the German Baltic Sea. Furthermore, to our knowledge, this is the first report of porpoise aggression by a socially isolated bottlenose dolphin.
KW  - Cetaceans
KW  - Interspecific aggression
KW  - Porpicide
KW  - Blunt trauma
KW  - Mortality
KW  - Stranding
Y1  - 2020
U6  - https://doi.org/10.1186/s40850-020-00061-7
SN  - 2056-3132
VL  - 5
IS  - 1
PB  - BMC
CY  - London
ER  - 
TY  - JOUR
A1  - Krüger, Johanna
A1  - Foerster, Verena Elisabeth
A1  - Trauth, Martin H.
A1  - Hofreiter, Michael
A1  - Tiedemann, Ralph
T1  - Exploring the Past Biosphere of Chew Bahir/Southern Ethiopia: Cross-Species Hybridization Capture of Ancient Sedimentary DNA from a Deep Drill Core
JF  - Frontiers in Earth Science
N2  - Eastern Africa has been a prime target for scientific drilling because it is rich in key paleoanthropological sites as well as in paleolakes, containing valuable paleoclimatic information on evolutionary time scales. The Hominin Sites and Paleolakes Drilling Project (HSPDP) explores these paleolakes with the aim of reconstructing environmental conditions around critical episodes of hominin evolution. Identification of biological taxa based on their sedimentary ancient DNA (sedaDNA) traces can contribute to understand past ecological and climatological conditions of the living environment of our ancestors. However, sedaDNA recovery from tropical environments is challenging because high temperatures, UV irradiation, and desiccation result in highly degraded DNA. Consequently, most of the DNA fragments in tropical sediments are too short for PCR amplification. We analyzed sedaDNA in the upper 70 m of the composite sediment core of the HSPDP drill site at Chew Bahir for eukaryotic remnants. We first tested shotgun high throughput sequencing which leads to metagenomes dominated by bacterial DNA of the deep biosphere, while only a small fraction was derived from eukaryotic, and thus probably ancient, DNA. Subsequently, we performed cross-species hybridization capture of sedaDNA to enrich ancient DNA (aDNA) from eukaryotic remnants for paleoenvironmental analysis, using established barcoding genes (cox1 and rbcL for animals and plants, respectively) from 199 species that may have had relatives in the past biosphere at Chew Bahir. Metagenomes yielded after hybridization capture are richer in reads with similarity to cox1 and rbcL in comparison to metagenomes without prior hybridization capture. Taxonomic assignments of the reads from these hybridization capture metagenomes also yielded larger fractions of the eukaryotic domain. For reads assigned to cox1, inferred wet periods were associated with high inferred relative abundances of putative limnic organisms (gastropods, green algae), while inferred dry periods showed increased relative abundances for insects. These findings indicate that cross-species hybridization capture can be an effective approach to enhance the information content of sedaDNA in order to explore biosphere changes associated with past environmental conditions, enabling such analyses even under tropical conditions.
KW  - Chew Bahir
KW  - hybridization capture
KW  - ICDP
KW  - paleoclimate
KW  - past biosphere
KW  - sedaDNA
KW  - sediment core
Y1  - 2021
U6  - https://doi.org/10.3389/feart.2021.683010
SN  - 2296-6463
SP  - 1
EP  - 20
PB  - Frontiers in Earth Science
CY  - Lausanne, Schweiz
ER  - 
TY  - JOUR
A1  - Weyrich, Alexandra
A1  - Jeschek, Marie
A1  - Schrapers, Katharina T.
A1  - Lenz, Dorina
A1  - Chung, Tzu Hung
A1  - Ruebensam, Kathrin
A1  - Yasar, Sermin
A1  - Schneemann, Markus
A1  - Ortmann, Sylvia
A1  - Jewgenow, Katarina
A1  - Fickel, Jörns
T1  - Diet changes alter paternally inherited epigenetic pattern in male Wild guinea pigs
JF  - Environmental Epigenetics
N2  - Epigenetic modifications, of which DNA methylation is the most stable, are a mechanism conveying environmental information to subsequent generations via parental germ lines. The paternal contribution to adaptive processes in the offspring might be crucial, but has been widely neglected in comparison to the maternal one. To address the paternal impact on the offspring’s adaptability to changes in diet composition, we investigated if low protein diet (LPD) in F0 males caused epigenetic alterations in their subsequently sired sons. We therefore fed F0 male Wild guinea pigs with a diet lowered in protein content (LPD) and investigated DNA methylation in sons sired before and after their father’s LPD treatment in both, liver and testis tissues. Our results point to a ‘heritable epigenetic response’ of the sons to the fathers’ dietary change. Because we detected methylation changes also in the testis tissue, they are likely to be transmitted to the F2 generation. Gene-network analyses of differentially methylated genes in liver identified main metabolic pathways indicating a metabolic reprogramming (‘metabolic shift’). Epigenetic mechanisms, allowing an immediate and inherited adaptation may thus be important for the survival of species in the context of a persistently changing environment, such as climate change.
KW  - DNA methylation
KW  - exposure
KW  - wild mammal species
KW  - inheritance
KW  - plasticity
KW  - adaptation
Y1  - 2018
U6  - https://doi.org/10.1093/eep/dvy011
SN  - 2058-5888
VL  - 4
IS  - 2
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Weyrich, Alexandra
A1  - Lenz, Dorina
A1  - Fickel, Jörns
T1  - Environmental Change-Dependent Inherited Epigenetic Response
JF  - GENES
N2  - Epigenetic modifications are a mechanism conveying environmental information to subsequent generations via parental germ lines. Research on epigenetic responses to environmental changes in wild mammals has been widely neglected, as well as studies that compare responses to changes in different environmental factors. Here, we focused on the transmission of DNA methylation changes to naive male offspring after paternal exposure to either diet (~40% less protein) or temperature increase (10 °C increased temperature). Because both experiments focused on the liver as the main metabolic and thermoregulation organ, we were able to decipher if epigenetic changes differed in response to different environmental changes. Reduced representation bisulfite sequencing (RRBS) revealed differentially methylated regions (DMRs) in annotated genomic regions in sons sired before (control) and after the fathers’ treatments. We detected both a highly specific epigenetic response dependent on the environmental factor that had changed that was reflected in genes involved in specific metabolic pathways, and a more general response to changes in outer stimuli reflected by epigenetic modifications in a small subset of genes shared between both responses. Our results indicated that fathers prepared their offspring for specific environmental changes by paternally inherited epigenetic modifications, suggesting a strong paternal contribution to adaptive processes.
KW  - DNA methylation
KW  - exposure
KW  - wild mammal species
KW  - inheritance
KW  - plasticity
KW  - adaptation
KW  - RRBS
Y1  - 2018
U6  - https://doi.org/10.3390/genes10010004
SN  - 2073-4425
VL  - 10
IS  - 1
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Koonce, Michael
A1  - Tikhonenko, Irina
A1  - Gräf, Ralph
T1  - Dictyostelium cell fixation
BT  - two simple tricks
JF  - Methods and protocols
N2  - We share two simple modifications to enhance the fixation and imaging of relatively small, motile, and rounded model cells. These include cell centrifugation and the addition of trace amounts of glutaraldehyde to existing fixation methods. Though they need to be carefully considered in each context, they have been useful to our studies of the spatial relationships of the microtubule cytoskeletal system.
KW  - Dictyostelium
KW  - cell fixation
KW  - microscopy
KW  - microtubule
KW  - cytoskeleton
Y1  - 2020
U6  - https://doi.org/10.3390/mps3030047
SN  - 2409-9279
VL  - 3
IS  - 3
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Banerjee, Pallavi
A1  - Lipowsky, Reinhard
A1  - Santer, Mark
T1  - Coarse-grained molecular model for the Glycosylphosphatidylinositol anchor with and without protein
JF  - Journal of Chemical Theory and Computation
N2  - Glycosylphosphatidylinositol (GPI) anchors are a unique class of complex glycolipids that anchor a great variety of proteins to the extracellular leaflet of plasma membranes of eukaryotic cells. These anchors can exist either with or without an attached protein called GPI-anchored protein (GPI-AP) both in vitro and in vivo. Although GPIs are known to participate in a broad range of cellular functions, it is to a large extent unknown how these are related to GPI structure and composition. Their conformational flexibility and microheterogeneity make it difficult to study them experimentally. Simplified atomistic models are amenable to all-atom computer simulations in small lipid bilayer patches but not suitable for studying their partitioning and trafficking in complex and heterogeneous membranes. Here, we present a coarse-grained model of the GPI anchor constructed with a modified version of the MARTINI force field that is suited for modeling carbohydrates, proteins, and lipids in an aqueous environment using MARTINI's polarizable water. The nonbonded interactions for sugars were reparametrized by calculating their partitioning free energies between polar and apolar phases. In addition, sugar-sugar interactions were optimized by adjusting the second virial coefficients of osmotic pressures for solutions of glucose, sucrose, and trehalose to match with experimental data. With respect to the conformational dynamics of GPI-anchored green fluorescent protein, the accessible time scales are now at least an order of magnitude larger than for the all-atom system. This is particularly important for fine-tuning the mutual interactions of lipids, carbohydrates, and amino acids when comparing to experimental results. We discuss the prospective use of the coarse-grained GPI model for studying protein-sorting and trafficking in membrane models.
KW  - Martini force-field
KW  - osmotic-pressure
KW  - potential-functions
KW  - aqueous-solution
KW  - dynamics
KW  - coefficient
KW  - simulation
KW  - trypanosoma
KW  - transition
KW  - parameters
Y1  - 2020
U6  - https://doi.org/10.1021/acs.jctc.0c00056
SN  - 1549-9626
SN  - 1549-9618
VL  - 16
IS  - 6
PB  - ACS Publications
CY  - Washington DC
ER  - 
TY  - JOUR
A1  - Canitz, Julia
A1  - Kirschbaum, Frank
A1  - Tiedemann, Ralph
T1  - Transcriptome-wide single nucleotide polymorphisms related to electric organ discharge differentiation among African weakly electric fish species
JF  - PLoS one
N2  - African weakly electric fish of the mormyrid genus Campylomormyrus generate pulse-type electric organ discharges (EODs) for orientation and communication. Their pulse durations are species-specific and elongated EODs are a derived trait. So far, differential gene expression among tissue-specific transcriptomes across species with different pulses and point mutations in single ion channel genes indicate a relation of pulse duration and electrocyte geometry/excitability. However, a comprehensive assessment of expressed Single Nucleotide Polymorphisms (SNPs) throughout the entire transcriptome of African weakly electric fish, with the potential to identify further genes influencing EOD duration, is still lacking. This is of particular value, as discharge duration is likely based on multiple cellular mechanisms and various genes. Here we provide the first transcriptome-wide SNP analysis of African weakly electric fish species (genus Campylomormyrus) differing by EOD duration to identify candidate genes and cellular mechanisms potentially involved in the determination of an elongated discharge of C. tshokwe. Non-synonymous substitutions specific to C. tshokwe were found in 27 candidate genes with inferred positive selection among Campylomormyrus species. These candidate genes had mainly functions linked to transcriptional regulation, cell proliferation and cell differentiation. Further, by comparing gene annotations between C. compressirostris (ancestral short EOD) and C. tshokwe (derived elongated EOD), we identified 27 GO terms and 2 KEGG pathway categories for which C. tshokwe significantly more frequently exhibited a species-specific expressed substitution than C. compressirostris. The results indicate that transcriptional regulation as well cell proliferation and differentiation take part in the determination of elongated pulse durations in C. tshokwe. Those cellular processes are pivotal for tissue morphogenesis and might determine the shape of electric organs supporting the observed correlation between electrocyte geometry/tissue structure and discharge duration. The inferred expressed SNPs and their functional implications are a valuable resource for future investigations on EOD durations.
Y1  - 2020
U6  - https://doi.org/10.1371/journal.pone.0240812
SN  - 1932-6203
VL  - 15
IS  - 10
PB  - PLoS
CY  - San Francisco, California, US
ER  - 
TY  - JOUR
A1  - Kolyvushko, Oleksandr
A1  - Latzke, Juliane
A1  - Dahmani, Ismail
A1  - Osterrieder, Nikolaus
A1  - Chiantia, Salvatore
A1  - Azab, Walid
T1  - Differentially-charged liposomes interact with alphaherpesviruses and interfere with virus entry
JF  - Pathogens
N2  - Exposure of phosphatidylserine (PS) in the outer leaflet of the plasma membrane is induced by infection with several members of the Alphaherpesvirinae subfamily. There is evidence that PS is used by the equine herpesvirus type 1 (EHV-1) during entry, but the exact role of PS and other phospholipids in the entry process remains unknown. Here, we investigated the interaction of differently charged phospholipids with virus particles and determined their influence on infection. Our data show that liposomes containing negatively charged PS or positively charged DOTAP (N-[1-(2,3-Dioleoyloxy)propyl]-N,N,N-trimethylammonium) inhibited EHV-1 infection, while neutral phosphatidylcholine (PC) had no effect. Inhibition of infection with PS was transient, decreased with time, and was dose dependent. Our findings indicate that both cationic and anionic phospholipids can interact with the virus and reduce infectivity, while, presumably, acting through different mechanisms. Charged phospholipids were found to have antiviral effects and may be used to inhibit EHV-1 infection.
KW  - alphaherpesvirus
KW  - EHV-1
KW  - phosphatidylserine
KW  - inhibition
KW  - pathogen host
KW  - interaction
Y1  - 2020
U6  - https://doi.org/10.3390/pathogens9050359
SN  - 2076-0817
VL  - 9
IS  - 5
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Mendel, Ralf R.
A1  - Hercher, Thomas W.
A1  - Zupok, Arkadiusz
A1  - Hasnat, Muhammad Abrar
A1  - Leimkühler, Silke
T1  - The requirement of inorganic Fe-S clusters for the biosynthesis of the organometallic molybdenum cofactor
JF  - Inorganics : open access journal
N2  - Iron-sulfur (Fe-S) clusters are essential protein cofactors. In enzymes, they are present either in the rhombic [2Fe-2S] or the cubic [4Fe-4S] form, where they are involved in catalysis and electron transfer and in the biosynthesis of metal-containing prosthetic groups like the molybdenum cofactor (Moco). Here, we give an overview of the assembly of Fe-S clusters in bacteria and humans and present their connection to the Moco biosynthesis pathway. In all organisms, Fe-S cluster assembly starts with the abstraction of sulfur froml-cysteine and its transfer to a scaffold protein. After formation, Fe-S clusters are transferred to carrier proteins that insert them into recipient apo-proteins. In eukaryotes like humans and plants, Fe-S cluster assembly takes place both in mitochondria and in the cytosol. Both Moco biosynthesis and Fe-S cluster assembly are highly conserved among all kingdoms of life. Moco is a tricyclic pterin compound with molybdenum coordinated through its unique dithiolene group. Moco biosynthesis begins in the mitochondria in a Fe-S cluster dependent step involving radical/S-adenosylmethionine (SAM) chemistry. An intermediate is transferred to the cytosol where the dithiolene group is formed, to which molybdenum is finally added. Further connections between Fe-S cluster assembly and Moco biosynthesis are discussed in detail.
KW  - Moco biosynthesis
KW  - Fe-S cluster assembly
KW  - l-cysteine desulfurase
KW  - ISC
KW  - SUF
KW  - NIF
KW  - iron
KW  - molybdenum
KW  - sulfur
Y1  - 2020
U6  - https://doi.org/10.3390/inorganics8070043
SN  - 2304-6740
VL  - 8
IS  - 7
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Potts, Jonathan R.
A1  - Schlägel, Ulrike E.
T1  - Parametrizing diffusion-taxis equations from animal movement trajectories using step selection analysis
JF  - Methods in ecology and evolution : an official journal of the British Ecological Society
N2  - Mathematical analysis of partial differential equations (PDEs) has led to many insights regarding the effect of organism movements on spatial population dynamics. However, their use has mainly been confined to the community of mathematical biologists, with less attention from statistical and empirical ecologists. We conjecture that this is principally due to the inherent difficulties in fitting PDEs to data. To help remedy this situation, in the context of movement ecology, we show how the popular technique of step selection analysis (SSA) can be used to parametrize a class of PDEs, calleddiffusion-taxismodels, from an animal's trajectory. We examine the accuracy of our technique on simulated data, then demonstrate the utility of diffusion-taxis models in two ways. First, for non-interacting animals, we derive the steady-state utilization distribution in a closed analytic form. Second, we give a recipe for deriving spatial pattern formation properties that emerge from interacting animals: specifically, do those interactions cause heterogeneous spatial distributions to emerge and if so, do these distributions oscillate at short times or emerge without oscillations? The second question is applied to data on concurrently tracked bank volesMyodes glareolus. Our results show that SSA can accurately parametrize diffusion-taxis equations from location data, providing the frequency of the data is not too low. We show that the steady-state distribution of our diffusion-taxis model, where it is derived, has an identical functional form to the utilization distribution given by resource selection analysis (RSA), thus formally linking (fine scale) SSA with (broad scale) RSA. For the bank vole data, we show how our SSA-PDE approach can give predictions regarding the spatial aggregation and segregation of different individuals, which are difficult to predict purely by examining results of SSA. Our methods provide a user-friendly way into the world of PDEs, via a well-used statistical technique, which should lead to tighter links between the findings of mathematical ecology and observations from empirical ecology. By providing a non-speculative link between observed movement behaviours and space use patterns on larger spatio-temporal scales, our findings will also aid integration of movement ecology into understanding spatial species distributions.
KW  - advection-diffusion
KW  - animal movement
KW  - home range
KW  - movement ecology
KW  - partial differential equations
KW  - resource selection
KW  - step selection
KW  - taxis
Y1  - 2020
U6  - https://doi.org/10.1111/2041-210X.13406
SN  - 2041-210X
VL  - 11
IS  - 9
SP  - 1092
EP  - 1105
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Heinze, Johannes
T1  - Herbivory by aboveground insects impacts plant root morphological traits
JF  - Plant ecology : an international journal
N2  - Aboveground herbivory induces physiological responses, like the release of belowground chemical defense and storage of secondary metabolites, as well as physical responses in plants, like increased root biomass production. However, studies on effects of aboveground herbivory on root morphology are scarce and until now no study tested herbivory effects under natural conditions for a large set of plant species. Therefore, in a field experiment on plant-soil interactions, I investigated the effect of aboveground insect herbivory on root morphological traits of 20 grassland plant species. For 9 of the 20 species, all individuals showed shoot damage in the presence of insect herbivores, but no damage in insect herbivore exclusions. In these 9 species root biomass increased and root morphological traits changed under herbivory towards thinner roots with increased specific root surface. In contrast, the remaining species did not differ in the number of individuals damaged, root biomass nor morphological traits with herbivores present vs. absent. The fact that aboveground herbivory resulted in thinner roots with increased specific root surface area for all species in which the herbivore exclusion manipulation altered shoot damage might indicate that plants increase nutrient uptake in response to herbivory. However, more importantly, results provide empirical evidence that aboveground herbivory impacts root morphological traits of plants. As these traits are important for the occupation of soil space, uptake processes, decomposition and interactions with soil biota, results suggest that herbivory-induced changes in root morphology might be of importance for plant-soil feedbacks and plant-plant competition.
KW  - herbivory
KW  - root traits
KW  - specific root length
KW  - specific root surface
KW  - area
KW  - plant-soil feedback
KW  - competition
Y1  - 2020
U6  - https://doi.org/10.1007/s11258-020-01045-w
SN  - 1385-0237
SN  - 1573-5052
VL  - 221
IS  - 8
SP  - 725
EP  - 732
PB  - Springer
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Pitzen, Valentin
A1  - Askarzada, Sophie
A1  - Gräf, Ralph
A1  - Meyer, Irene
T1  - CDK5RAP2 Is an Essential Scaffolding Protein of the Corona of the Dictyostelium Centrosome
JF  - Cells
N2  - Dictyostelium centrosomes consist of a nucleus-associated cylindrical, three-layered core structure surrounded by a corona consisting of microtubule-nucleation complexes embedded in a scaffold of large coiled-coil proteins. One of them is the conserved CDK5RAP2 protein. Here we focus on the role of Dictyostelium CDK5RAP2 for maintenance of centrosome integrity, its interaction partners and its dynamic behavior during interphase and mitosis. GFP-CDK5RAP2 is present at the centrosome during the entire cell cycle except from a short period during prophase, correlating with the normal dissociation of the corona at this stage. RNAi depletion of CDK5RAP2 results in complete disorganization of centrosomes and microtubules suggesting that CDK5RAP2 is required for organization of the corona and its association to the core structure. This is in line with the observation that overexpressed GFP-CDK5RAP2 elicited supernumerary cytosolic MTOCs. The phenotype of CDK5RAP2 depletion was very reminiscent of that observed upon depletion of CP148, another scaffolding protein of the corona. BioID interaction assays revealed an interaction of CDK5RAP2 not only with the corona markers CP148, gamma-tubulin, and CP248, but also with the core components Cep192, CP75, and CP91. Furthermore, protein localization studies in both depletion strains revealed that CP148 and CDK5RAP2 cooperate in corona organization.
KW  - centrosome
KW  - centriole
KW  - Dictyostelium
KW  - microtubules
KW  - mitosis
Y1  - 2018
U6  - https://doi.org/10.3390/cells7040032
SN  - 2073-4409
VL  - 7
IS  - 4
PB  - MDPI
CY  - Basel
ER  - 
TY  - GEN
A1  - Gräf, Ralph
T1  - Comparative Biology of Centrosomal Structures in Eukaryotes
T2  - Cells
N2  - The centrosome is not only the largest and most sophisticated protein complex within a eukaryotic cell, in the light of evolution, it is also one of its most ancient organelles. This special issue of "Cells" features representatives of three main, structurally divergent centrosome types, i.e., centriole-containing centrosomes, yeast spindle pole bodies (SPBs), and amoebozoan nucleus-associated bodies (NABs). Here, I discuss their evolution and their key-functions in microtubule organization, mitosis, and cytokinesis. Furthermore, I provide a brief history of centrosome research and highlight recently emerged topics, such as the role of centrioles in ciliogenesis, the relationship of centrosomes and centriolar satellites, the integration of centrosomal structures into the nuclear envelope and the involvement of centrosomal components in non-centrosomal microtubule organization.
KW  - centrosome
KW  - centriole
KW  - cilium
KW  - basal body
KW  - spindle pole body
KW  - SPB
KW  - nucleus-associated body
KW  - NAB
KW  - microtubules
Y1  - 2018
U6  - https://doi.org/10.3390/cells7110202
SN  - 2073-4409
VL  - 7
IS  - 11
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Grafe, Marianne
A1  - Hofmann, Phillip
A1  - Batsios, Petros
A1  - Meyer, Irene
A1  - Gräf, Ralph
T1  - In vivo assembly of a Dictyostelium lamin mutant induced by light, mechanical stress, and pH
JF  - Cells
N2  - We expressed Dictyostelium lamin (NE81) lacking both a functional nuclear localization signal and a CAAX-box for C-terminal lipid modification. This lamin mutant assembled into supramolecular, three-dimensional clusters in the cytosol that disassembled at the onset of mitosis and re-assembled in late telophase, thus mimicking the behavior of the endogenous protein. As disassembly is regulated by CDK1-mediated phosphorylation at serine 122, we generated a phosphomimetic S122E mutant called GFP-NE81-S122E-∆NLS∆CLIM. Surprisingly, during imaging, the fusion protein assembled into cytosolic clusters, similar to the protein lacking the phosphomimetic mutation. Clusters disassembled again in the darkness. Assembly could be induced with blue but not green or near ultraviolet light, and it was independent of the fusion tag. Assembly similarly occurred upon cell flattening. Earlier reports and own observations suggested that both blue light and cell flattening could result in a decrease of intracellular pH. Indeed, keeping the cells at low pH also reversibly induced cluster formation. Our results indicate that lamin assembly can be induced by various stress factors and that these are transduced via intracellular acidification. Although these effects have been shown in a phosphomimetic CDK1 mutant of the Dictyostelium lamin, they are likely relevant also for wild-type lamin.
KW  - lamin
KW  - NE81
KW  - Dictyostelium
KW  - nuclear envelope
KW  - nuclear lamina
Y1  - 2020
VL  - 9
IS  - 8
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Batsios, Petros
A1  - Gräf, Ralph
A1  - Koonce, Michael P.
A1  - Larochelle, Denis A.
A1  - Meyer, Irene
T1  - Nuclear envelope organization in Dictyostelium discoideum
JF  - The international journal of developmental biology
N2  - The nuclear envelope consists of the outer and the inner nuclear membrane, the nuclear lamina and the nuclear pore complexes, which regulate nuclear import and export.The major constituent of the nuclear lamina of Dictyostelium is the lamin NE81. It can form filaments like B-type lamins and it interacts with Sun 1, as well as with the LEM/HeH-family protein Src1. Sun 1 and Src1 are nuclear envelope transmembrane proteins involved in the centrosome-nucleus connection and nuclear envelope stability at the nucleolar regions, respectively. In conjunction with a KASH-domain protein, Sun 1 usually forms a so-called LINC complex.Two proteins with functions reminiscent of KASH-domain proteins at the outer nuclear membrane of Dictyostelium are known; interaptin which serves as an actin connector and the kinesin Kif9 which plays a role in the microtubule-centrosome connector. However, both of these lack the conserved KASH-domain. The link of the centrosome to the nuclear envelope is essential for the insertion of the centrosome into the nuclear envelope and the appropriate spindle formation. Moreover, centrosome insertion is involved in perm eabilization of the mitotic nucleus, which ensures access of tubulin dimers and spindle assembly factors. Our recent progress in identifying key molecular players at the nuclear envelope of Dictyostelium promises further insights into the mechanisms of nuclear envelope dynamics.
KW  - nuclear envelop
KW  - Dictyostelium
KW  - lamin
KW  - NET
KW  - centrosome
KW  - centromere
Y1  - 2019
U6  - https://doi.org/10.1387/ijdb.190184rg
SN  - 0214-6282
SN  - 1696-3547
VL  - 63
IS  - 8-10
SP  - 509
EP  - 519
PB  - UBC Pr
CY  - Bilbao
ER  - 
TY  - JOUR
A1  - Gräf, Ralph
A1  - Grafe, Marianne
A1  - Meyer, Irene
A1  - Mitic, Kristina
A1  - Pitzen, Valentin
T1  - The dictyostelium centrosome
JF  - Cells : open access journal
N2  - The centrosome of Dictyostelium amoebae contains no centrioles and consists of a cylindrical layered core structure surrounded by a corona harboring microtubule-nucleating gamma-tubulin complexes. It is the major centrosomal model beyond animals and yeasts. Proteomics, protein interaction studies by BioID and superresolution microscopy methods led to considerable progress in our understanding of the composition, structure and function of this centrosome type. We discuss all currently known components of the Dictyostelium centrosome in comparison to other centrosomes of animals and yeasts.
KW  - microtubule-organizing center
KW  - microtubule-organization
KW  - centrosome
KW  - Dictyostelium
KW  - mitosis
Y1  - 2021
U6  - https://doi.org/10.3390/cells10102657
SN  - 2073-4409
VL  - 10
IS  - 10
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Schroedter, Linda
A1  - Schneider, Roland
A1  - Remus, Lisa
A1  - Venus, Joachim
T1  - L-(+)-lactic acid from reed
BT  - comparing various resources for the nutrient provision of B. coagulans
JF  - Resources
N2  - Biotechnological production of lactic acid (LA) is based on the so-called first generation feedstocks, meaning sugars derived from food and feed crops such as corn, sugarcane and cassava. The aim of this study was to exploit the potential of a second generation resource: Common reed (Phragmites australis) is a powerfully reproducing sweet grass which grows in wetlands and creates vast monocultural populations. This lignocellulose biomass bears the possibility to be refined to value-added products, without competing with agro industrial land. Besides utilizing reed as a renewable and inexpensive substrate, low-cost nutritional supplementation was analyzed for the fermentation of thermophilicBacilluscoagulans.Various nutritional sources such as baker's and brewer's yeast, lucerne green juice and tryptone were investigated for the replacement of yeast extract. The structure of the lignocellulosic material was tackled by chemical treatment (1% NaOH) and enzymatic hydrolysis (Cellic(R)CTec2).B.coagulansDSM ID 14-300 was employed for the homofermentative conversion of the released hexose and pentose sugars to polymerizable L-(+)-LA of over 99.5% optical purity. The addition of autolyzed baker's yeast led to the best results of fermentation, enabling an LA titer of 28.3 g L(-1)and a yield of 91.6%.
KW  - lignocellulose
KW  - reed
KW  - Phragmites australis
KW  - lactic acid
KW  - Bacillus
KW  - coagulans
Y1  - 2020
U6  - https://doi.org/10.3390/resources9070089
SN  - 2079-9276
VL  - 9
IS  - 7
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Yarman, Aysu
A1  - Jetzschmann, Katharina J.
A1  - Neumann, Bettina
A1  - Zhang, Xiaorong
A1  - Wollenberger, Ulla
A1  - Cordin, Aude
A1  - Haupt, Karsten
A1  - Scheller, Frieder W.
T1  - Enzymes as Tools in MIP-Sensors
JF  - Chemosensors
N2  - Molecularly imprinted polymers (MIPs) have the potential to complement antibodies in bioanalysis, are more stable under harsh conditions, and are potentially cheaper to produce. However, the affinity and especially the selectivity of MIPs are in general lower than those of their biological pendants. Enzymes are useful tools for the preparation of MIPs for both low and high-molecular weight targets: As a green alternative to the well-established methods of chemical polymerization, enzyme-initiated polymerization has been introduced and the removal of protein templates by proteases has been successfully applied. Furthermore, MIPs have been coupled with enzymes in order to enhance the analytical performance of biomimetic sensors: Enzymes have been used in MIP-sensors as tracers for the generation and amplification of the measuring signal. In addition, enzymatic pretreatment of an analyte can extend the analyte spectrum and eliminate interferences.
KW  - enzymatic MIP synthesis
KW  - template digestion
KW  - enzyme tracer
KW  - enzymatic analyte conversion
KW  - molecularly imprinted polymers
Y1  - 2017
U6  - https://doi.org/10.3390/chemosensors5020011
SN  - 2227-9040
VL  - 5
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Thomas, Jessica E.
A1  - Carvalho, Gary R.
A1  - Haile, James
A1  - Martin, Michael D.
A1  - Castruita, Jose A. Samaniego
A1  - Niemann, Jonas
A1  - Sinding, Mikkel-Holger S.
A1  - Sandoval-Velasco, Marcela
A1  - Rawlence, Nicolas J.
A1  - Fuller, Errol
A1  - Fjeldsa, Jon
A1  - Hofreiter, Michael
A1  - Stewart, John R.
A1  - Gilbert, M. Thomas P.
A1  - Knapp, Michael
T1  - An ‛Aukward’ tale
BT  - a genetic approach to discover the whereabouts of the  Last Great Auks
JF  - Genes
N2  - One hundred and seventy-three years ago, the last two Great Auks, Pinguinus impennis, ever reliably seen were killed. Their internal organs can be found in the collections of the Natural History Museum of Denmark, but the location of their skins has remained a mystery. In 1999, Great Auk expert Errol Fuller proposed a list of five potential candidate skins in museums around the world. Here we take a palaeogenomic approach to test which—if any—of Fuller’s candidate skins likely belong to either of the two birds. Using mitochondrial genomes from the five candidate birds (housed in museums in Bremen, Brussels, Kiel, Los Angeles, and Oldenburg) and the organs of the last two known individuals, we partially solve the mystery that has been on Great Auk scholars’ minds for generations and make new suggestions as to the whereabouts of the still-missing skin from these two birds.
KW  - ancient DNA
KW  - extinct birds
KW  - mitochondrial genome
KW  - museum specimens
KW  - palaeogenomics
Y1  - 2017
U6  - https://doi.org/10.3390/genes8060164
SN  - 2073-4425
VL  - 8
IS  - 6
SP  - 164
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Gisder, Sebastian
A1  - Schüler, Vivian
A1  - Horchler, Lennart L.
A1  - Groth, Detlef
A1  - Genersch, Elke
T1  - Long-Term Temporal Trends of Nosema spp. Infection Prevalence in Northeast Germany
BT  - Continuous Spread of Nosema ceranae, an Emerging Pathogen of Honey Bees (Apis mellifera), but No General Replacement of Nosema apis
JF  - Frontiers in cellular and infection microbiology
N2  - The Western honey bee (Apis mellifera) is widely used as commercial pollinator in worldwide agriculture and, therefore, plays an important role in global food security. Among the parasites and pathogens threatening health and survival of honey bees are two species of microsporidia, Nosema apis and Nosema ceranae. Nosema ceranae is considered an emerging pathogen of the Western honey bee. Reports on the spread of N. ceranae suggested that this presumably highly virulent species is replacing its more benign congener N. apis in the global A. mellifera population. We here present a 12 year longitudinal cohort study on the prevalence of N. apis and N. ceranae in Northeast Germany. Between 2005 and 2016, a cohort of about 230 honey bee colonies originating from 23 apiaries was sampled twice a year (spring and autumn) resulting in a total of 5,600 bee samples which were subjected to microscopic and molecular analysis for determining the presence of infections with N. apis or/and N. ceranae. Throughout the entire study period, both N. apis- and N. ceranae-infections could be diagnosed within the cohort. Logistic regression analysis of the prevalence data demonstrated a significant increase of N. ceranae-infections over the last 12 years, both in autumn (reflecting the development during the summer) and in spring (reflecting the development over winter) samples. Cell culture experiments confirmed that N. ceranae has a higher proliferative potential than N. apis at 27. and 33 degrees C potentially explaining the increase in N. ceranae prevalence during summer. In autumn, characterized by generally low infection prevalence, this increase was accompanied by a significant decrease in N. apis- infection prevalence. In contrast, in spring, the season with a higher prevalence of infection, no significant decrease of N. apis infections despite a significant increase in N. ceranae infections could be observed. Therefore, our data do not support a general advantage of N. ceranae over N. apis and an overall replacement of N. apis by N. ceranae in the studied honey bee population.
KW  - honey bee
KW  - Apis mellifera
KW  - Nosema spp.
KW  - epidemiology
KW  - replacement
Y1  - 2017
U6  - https://doi.org/10.3389/fcimb.2017.00301
SN  - 2235-2988
VL  - 7
PB  - Frontiers Research Foundation
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Noonan, Michael J.
A1  - Fleming, Christen H.
A1  - Tucker, Marlee A.
A1  - Kays, Roland
A1  - Harrison, Autumn-Lynn
A1  - Crofoot, Margaret C.
A1  - Abrahms, Briana
A1  - Alberts, Susan C.
A1  - Ali, Abdullahi H.
A1  - Blaum, Niels
T1  - Effects of body size on estimation of mammalian area requirements
JF  - Conservation Biology
N2  - Accurately quantifying species' area requirements is a prerequisite for effective area-based conservation. This typically involves collecting tracking data on species of interest and then conducting home-range analyses. Problematically, autocorrelation in tracking data can result in space needs being severely underestimated. Based on the previous work, we hypothesized the magnitude of underestimation varies with body mass, a relationship that could have serious conservation implications. To evaluate this hypothesis for terrestrial mammals, we estimated home-range areas with global positioning system (GPS) locations from 757 individuals across 61 globally distributed mammalian species with body masses ranging from 0.4 to 4000 kg. We then applied block cross-validation to quantify bias in empirical home-range estimates. Area requirements of mammals <10 kg were underestimated by a mean approximately15%, and species weighing approximately100 kg were underestimated by approximately50% on average. Thus, we found area estimation was subject to autocorrelation-induced bias that was worse for large species. Combined with the fact that extinction risk increases as body mass increases, the allometric scaling of bias we observed suggests the most threatened species are also likely to be those with the least accurate home-range estimates. As a correction, we tested whether data thinning or autocorrelation-informed home-range estimation minimized the scaling effect of autocorrelation on area estimates. Data thinning required an approximately93% data loss to achieve statistical independence with 95% confidence and was, therefore, not a viable solution. In contrast, autocorrelation-informed home-range estimation resulted in consistently accurate estimates irrespective of mass. When relating body mass to home range size, we detected that correcting for autocorrelation resulted in a scaling exponent significantly >1, meaning the scaling of the relationship changed substantially at the upper end of the mass spectrum.
KW  - allometry
KW  - animal movement
KW  - area-based conservation
KW  - autocorrelation
KW  - home range
KW  - kernel density estimation
KW  - reserve design
KW  - scaling
Y1  - 2019
VL  - 34
IS  - 4
PB  - Wiley-Blackwell
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Schittko, Conrad
A1  - Bernard-Verdier, Maud
A1  - Heger, Tina
A1  - Buchholz, Sascha
A1  - Kowarik, Ingo
A1  - von der Lippe, Moritz
A1  - Seitz, Birgit
A1  - Joshi, Jasmin Radha
A1  - Jeschke, Jonathan M.
T1  - A multidimensional framework for measuring biotic novelty: How novel is a community?
JF  - Global Change Biology
N2  - Anthropogenic changes in climate, land use, and disturbance regimes, as well as introductions of non-native species can lead to the transformation of many ecosystems. The resulting novel ecosystems are usually characterized by species assemblages that have not occurred previously in a given area. Quantifying the ecological novelty of communities (i.e., biotic novelty) would enhance the understanding of environmental change. However, quantification remains challenging since current novelty metrics, such as the number and/or proportion of non-native species in a community, fall short of considering both functional and evolutionary aspects of biotic novelty. Here, we propose the Biotic Novelty Index (BNI), an intuitive and flexible multidimensional measure that combines (a) functional differences between native and non-native introduced species with (b) temporal dynamics of species introductions. We show that the BNI is an additive partition of Rao's quadratic entropy, capturing the novel interaction component of the community's functional diversity. Simulations show that the index varies predictably with the relative amount of functional novelty added by recently arrived species, and they illustrate the need to provide an additional standardized version of the index. We present a detailed R code and two applications of the BNI by (a) measuring changes of biotic novelty of dry grassland plant communities along an urbanization gradient in a metropolitan region and (b) determining the biotic novelty of plant species assemblages at a national scale. The results illustrate the applicability of the index across scales and its flexibility in the use of data of different quality. Both case studies revealed strong connections between biotic novelty and increasing urbanization, a measure of abiotic novelty. We conclude that the BNI framework may help building a basis for better understanding the ecological and evolutionary consequences of global change.
KW  - alien species
KW  - biological invasions
KW  - coexistence
KW  - ecological novelty
KW  - functional diversity
KW  - novel ecosystems
KW  - novel species
KW  - standard metrics
Y1  - 2019
VL  - 26
IS  - 8
PB  - John Wiley & Sons, Inc.
CY  - New Jersey
ER  - 
TY  - JOUR
A1  - König, Christian
A1  - Weigelt, Patrick
A1  - Taylor, Amanda
A1  - Stein, Anke
A1  - Dawson, Wayne
A1  - Essl, Franz
A1  - Pergl, Jan
A1  - Pyšek, Petr
A1  - Kleunen, Mark van
A1  - Winter, Marten
A1  - Chatelain, Cyrille
A1  - Wieringa, Jan J.
A1  - Krestov, Pavel
A1  - Kreft, Holger
T1  - Source pools and disharmony of the world’s island floras
JF  - Ecography
N2  - Island disharmony refers to the biased representation of higher taxa on islands compared to their mainland source regions and represents a central concept in island biology. Here, we develop a generalizable framework for approximating these source regions and conduct the first global assessment of island disharmony and its underlying drivers. We compiled vascular plant species lists for 178 oceanic islands and 735 mainland regions. Using mainland data only, we modelled species turnover as a function of environmental and geographic distance and predicted the proportion of shared species between each island and mainland region. We then quantified the over- or under-representation of families on individual islands (representational disharmony) by contrasting the observed number of species against a null model of random colonization from the mainland source pool, and analysed the effects of six family-level functional traits on the resulting measure. Furthermore, we aggregated the values of representational disharmony per island to characterize overall taxonomic bias of a given flora (compositional disharmony), and analysed this second measure as a function of four island biogeographical variables. Our results indicate considerable variation in representational disharmony both within and among plant families. Examples of generally over-represented families include Urticaceae, Convolvulaceae and almost all pteridophyte families. Other families such as Asteraceae and Orchidaceae were generally under-represented, with local peaks of over-representation in known radiation hotspots. Abiotic pollination and a lack of dispersal specialization were most strongly associated with an insular over-representation of families, whereas other family-level traits showed minor effects. With respect to compositional disharmony, large, high-elevation islands tended to have the most disharmonic floras. Our results provide important insights into the taxon- and island-specific drivers of disharmony. The proposed framework allows overcoming the limitations of previous approaches and provides a quantitative basis for incorporating functional and phylogenetic approaches into future studies of island disharmony.
KW  - assembly processes
KW  - biotic filtering
KW  - dispersal filtering
KW  - environmental filtering
KW  - generalized dissimilarity modelling
KW  - island disharmony
KW  - island syndromes
KW  - source regions
KW  - vascular plants
Y1  - 2020
VL  - 44
IS  - 1
PB  - Wiley-Blackwell
CY  - Oxford
ER  - 
TY  - JOUR
A1  - van Velzen, Ellen
A1  - Gaedke, Ursula
T1  - Reversed predator-prey cycles are driven by the amplitude of prey oscillations
JF  - Ecology and evolution
N2  - Ecoevolutionary feedbacks in predator-prey systems have been shown to qualitatively alter predator-prey dynamics. As a striking example, defense-offense coevolution can reverse predator-prey cycles, so predator peaks precede prey peaks rather than vice versa. However, this has only rarely been shown in either model studies or empirical systems. Here, we investigate whether this rarity is a fundamental feature of reversed cycles by exploring under which conditions they should be found. For this, we first identify potential conditions and parameter ranges most likely to result in reversed cycles by developing a new measure, the effective prey biomass, which combines prey biomass with prey and predator traits, and represents the prey biomass as perceived by the predator. We show that predator dynamics always follow the dynamics of the effective prey biomass with a classic 1/4-phase lag. From this key insight, it follows that in reversed cycles (i.e., -lag), the dynamics of the actual and the effective prey biomass must be in antiphase with each other, that is, the effective prey biomass must be highest when actual prey biomass is lowest, and vice versa. Based on this, we predict that reversed cycles should be found mainly when oscillations in actual prey biomass are small and thus have limited impact on the dynamics of the effective prey biomass, which are mainly driven by trait changes. We then confirm this prediction using numerical simulations of a coevolutionary predator-prey system, varying the amplitude of the oscillations in prey biomass: Reversed cycles are consistently associated with regions of parameter space leading to small-amplitude prey oscillations, offering a specific and highly testable prediction for conditions under which reversed cycles should occur in natural systems.
KW  - coevolution
KW  - ecoevolutionary dynamics
KW  - predator-prey dynamics
KW  - top-down control
Y1  - 2018
U6  - https://doi.org/10.1002/ece3.4184
SN  - 2045-7758
VL  - 8
IS  - 12
SP  - 6317
EP  - 6329
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Bolius, Sarah
A1  - Wiedner, Claudia
A1  - Weithoff, Guntram
T1  - Low invasion success of an invasive cyanobacterium in a chlorophyte dominated lake
JF  - Scientific reports
Y1  - 2019
SN  - 2045-2322
VL  - 9
PB  - Macmillan Publishers Limited
CY  - London
ER  - 
TY  - JOUR
A1  - Feiner, Rebecca Christine
A1  - Teschner, Julian
A1  - Teschner, Kathrin E.
A1  - Radukic, Marco T.
A1  - Baumann, Tobias
A1  - Hagen, Sven
A1  - Hannappel, Yvonne
A1  - Biere, Niklas
A1  - Anselmetti, Dario
A1  - Arndt, Katja Maren
A1  - Müller, Kristian Mark
T1  - rAAV Engineering for Capsid-Protein Enzyme Insertions and Mosaicism Reveals Resilience to Mutational, Structural and Thermal Perturbations
JF  - International journal of molecular sciences
N2  - Recombinant adeno-associated viruses (rAAV) provide outstanding options for customization and superior capabilities for gene therapy. To access their full potential, facile genetic manipulation is pivotal, including capsid loop modifications. Therefore, we assessed capsid tolerance to modifications of the structural VP proteins in terms of stability and plasticity. Flexible glycine-serine linkers of increasing sizes were, at the genetic level, introduced into the 587 loop region of the VP proteins of serotype 2, the best studied AAV representative. Analyses of biological function and thermal stability with respect to genome release of viral particles revealed structural plasticity. In addition, insertion of the 29 kDa enzyme beta-lactamase into the loop region was tested with a complete or a mosaic modification setting. For the mosaic approach, investigation of VP2 trans expression revealed that a Kozak sequence was required to prevent leaky scanning. Surprisingly, even the full capsid modification with beta-lactamase allowed for the assembly of capsids with a concomitant increase in size. Enzyme activity assays revealed lactamase functionality for both rAAV variants, which demonstrates the structural robustness of this platform technology.
KW  - adeno-associated-virus
KW  - beta-lactamase
KW  - inverted terminal repeat (ITR)
KW  - loop modification
KW  - capsid stability
Y1  - 2019
U6  - https://doi.org/10.3390/ijms20225702
SN  - 1422-0067
VL  - 20
IS  - 22
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Wu, Hao
A1  - Han, Yijie
A1  - Rodriguez Sillke, Yasmina
A1  - Deng, Hongzhang
A1  - Siddiqui, Sophiya
A1  - Treese, Christoph
A1  - Schmidt, Franziska
A1  - Friedrich, Marie
A1  - Keye, Jacqueline
A1  - Wan, Jiajia
A1  - Qin, Yue
A1  - Kühl, Anja A.
A1  - Qin, Zhihai
A1  - Siegmund, Britta
A1  - Glauben, Rainer
T1  - Lipid droplet-dependent fatty acid metabolism controls the immune suppressive phenotype of tumor-associated macrophages
JF  - EMBO molecular medicine
N2  - Tumor-associated macrophages (TAMs) promote tumor growth and metastasis by suppressing tumor immune surveillance. Herein, we provide evidence that the immunosuppressive phenotype of TAMs is controlled by long-chain fatty acid metabolism, specifically unsaturated fatty acids, here exemplified by oleate. Consequently, en-route enriched lipid droplets were identified as essential organelles, which represent effective targets for chemical inhibitors to block in vitro polarization of TAMs and tumor growth in vivo. In line, analysis of human tumors revealed that myeloid cells infiltrating colon cancer but not gastric cancer tissue indeed accumulate lipid droplets. Mechanistically, our data indicate that oleate-induced polarization of myeloid cells depends on the mammalian target of the rapamycin pathway. Thus, our findings reveal an alternative therapeutic strategy by targeting the pro-tumoral myeloid cells on a metabolic level.
KW  - cancer immunotherapy
KW  - lipid droplets
KW  - lipid metabolism
KW  - tumor microenvironment
KW  - tumor-associated macrophage
Y1  - 2019
U6  - https://doi.org/10.15252/emmm.201910698
SN  - 1757-4676
SN  - 1757-4684
VL  - 11
IS  - 11
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Kielar, Charlotte
A1  - Xin, Yang
A1  - Xu, Xiaodan
A1  - Zhu, Siqi
A1  - Gorin, Nelli
A1  - Grundmeier, Guido
A1  - Möser, Christin
A1  - Smith, David M.
A1  - Keller, Adrian
T1  - Effect of staple age on DNA origami nanostructure assembly and stability
JF  - Molecules
N2  - DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to real-world applications, such as nanoelectronics, drug delivery, and biosensing. While many of these real-world applications rely on an intact DNA origami shape, they often also subject the DNA origami nanostructures to rather harsh and potentially damaging environmental and processing conditions. Furthermore, in the context of DNA origami mass production, the long-term storage of DNA origami nanostructures or their pre-assembled components also becomes an issue of high relevance, especially regarding the possible negative effects on DNA origami structural integrity. Thus, we investigated the effect of staple age on the self-assembly and stability of DNA origami nanostructures using atomic force microscopy. Different harsh processing conditions were simulated by applying different sample preparation protocols. Our results show that staple solutions may be stored at -20 degrees C for several years without impeding DNA origami self-assembly. Depending on DNA origami shape and superstructure, however, staple age may have negative effects on DNA origami stability under harsh treatment conditions. Mass spectrometry analysis of the aged staple mixtures revealed no signs of staple fragmentation. We, therefore, attribute the increased DNA origami sensitivity toward environmental conditions to an accumulation of damaged nucleobases, which undergo weaker base-pairing interactions and thus lead to reduced duplex stability.
KW  - DNA origami
KW  - atomic force microscopy
KW  - stability
KW  - storage
Y1  - 2019
U6  - https://doi.org/10.3390/molecules24142577
SN  - 1420-3049
VL  - 24
IS  - 14
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Yan, Wenhao
A1  - Chen, Dijun
A1  - Schumacher, Julia
A1  - Durantini, Diego
A1  - Engelhorn, Julia
A1  - Chen, Ming
A1  - Carles, Cristel C.
A1  - Kaufmann, Kerstin
T1  - Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis
JF  - Nature Communications
N2  - Enhancers are critical for developmental stage-specific gene expression, but their dynamic regulation in plants remains poorly understood. Here we compare genome-wide localization of H3K27ac, chromatin accessibility and transcriptomic changes during flower development in Arabidopsis. H3K27ac prevalently marks promoter-proximal regions, suggesting that H3K27ac is not a hallmark for enhancers in Arabidopsis. We provide computational and experimental evidence to confirm that distal DNase. hypersensitive sites are predictive of enhancers. The predicted enhancers are highly stage-specific across flower development, significantly associated with SNPs for flowering-related phenotypes, and conserved across crucifer species. Through the integration of genome-wide transcription factor (TF) binding datasets, we find that floral master regulators and stage-specific TFs are largely enriched at developmentally dynamic enhancers. Finally, we show that enhancer clusters and intronic enhancers significantly associate with stage-specific gene regulation by floral master TFs. Our study provides insights into the functional flexibility of enhancers during plant development, as well as hints to annotate plant enhancers.
Y1  - 2019
U6  - https://doi.org/10.1038/s41467-019-09513-2
SN  - 2041-1723
VL  - 10
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Schieferdecker, Anne
A1  - Wendler, Petra
T1  - Structural Mapping of Missense Mutations in the Pex1/Pex6 Complex
JF  - International journal of molecular sciences
N2  - Peroxisome biogenesis disorders (PBDs) are nontreatable hereditary diseases with a broad range of severity. Approximately 65% of patients are affected by mutations in the peroxins Pex1 and Pex6. The proteins form the heteromeric Pex1/Pex6 complex, which is important for protein import into peroxisomes. To date, no structural data are available for this AAA+ ATPase complex. However, a wealth of information can be transferred from low-resolution structures of the yeast scPex1/scPex6 complex and homologous, well-characterized AAA+ ATPases. We review the abundant records of missense mutations described in PBD patients with the aim to classify and rationalize them by mapping them onto a homology model of the human Pex1/Pex6 complex. Several mutations concern functionally conserved residues that are implied in ATP hydrolysis and substrate processing. Contrary to fold destabilizing mutations, patients suffering from function-impairing mutations may not benefit from stabilizing agents, which have been reported as potential therapeutics for PBD patients.
KW  - Zellweger syndrome spectrum disorder (ZSSD)
KW  - Zellweger
KW  - structure
KW  - Pex1
KW  - Pex6
KW  - mutation
Y1  - 2019
U6  - https://doi.org/10.3390/ijms20153756
SN  - 1422-0067
VL  - 20
IS  - 15
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Chaturvedi, Neha
A1  - Mehrotra, Bagish
A1  - Kumari, Sangeeta
A1  - Gupta, Saurabh
A1  - Subramanya, Hosahalli
A1  - Saberwal, Gayatri
T1  - Some data quality issues at ClinicalTrials.gov
JF  - Trials
KW  - ClinicalTrials
KW  - gov
KW  - Drugs
KW  - Biologicals
KW  - Clinical trial
KW  - Principal Investigator
KW  - Data quality
KW  - Database errors
Y1  - 2019
U6  - https://doi.org/10.1186/s13063-019-3408-2
SN  - 1745-6215
VL  - 20
PB  - BMC
CY  - London
ER  - 
TY  - JOUR
A1  - Frommhold, Martin
A1  - Heim, Arend
A1  - Barabanov, Mikhail
A1  - Maier, Franziska
A1  - Mühle, Ralf-Udo
A1  - Smirenski, Sergei M.
A1  - Heim, Wieland
T1  - Breeding habitat and nest-site selection by an obligatory "nest-cleptoparasite", the Amur Falcon Falco amurensis
JF  - Ecology and evolution
N2  - The selection of a nest site is crucial for successful reproduction of birds. Animals which re-use or occupy nest sites constructed by other species often have limited choice. Little is known about the criteria of nest-stealing species to choose suitable nesting sites and habitats. Here, we analyze breeding-site selection of an obligatory "nest-cleptoparasite", the Amur Falcon Falco amurensis. We collected data on nest sites at Muraviovka Park in the Russian Far East, where the species breeds exclusively in nests of the Eurasian Magpie Pica pica. We sampled 117 Eurasian Magpie nests, 38 of which were occupied by Amur Falcons. Nest-specific variables were assessed, and a recently developed habitat classification map was used to derive landscape metrics. We found that Amur Falcons chose a wide range of nesting sites, but significantly preferred nests with a domed roof. Breeding pairs of Eurasian Hobby Falco subbuteo and Eurasian Magpie were often found to breed near the nest in about the same distance as neighboring Amur Falcon pairs. Additionally, the occurrence of the species was positively associated with bare soil cover, forest cover, and shrub patches within their home range and negatively with the distance to wetlands. Areas of wetlands and fallow land might be used for foraging since Amur Falcons mostly depend on an insect diet. Additionally, we found that rarely burned habitats were preferred. Overall, the effect of landscape variables on the choice of actual nest sites appeared to be rather small. We used different classification methods to predict the probability of occurrence, of which the Random forest method showed the highest accuracy. The areas determined as suitable habitat showed a high concordance with the actual nest locations. We conclude that Amur Falcons prefer to occupy newly built (domed) nests to ensure high nest quality, as well as nests surrounded by available feeding habitats.
KW  - cleptoparasitism
KW  - fire
KW  - habitat use
KW  - machine learning
KW  - magpie
KW  - nest-site selection
KW  - random forest
Y1  - 2019
U6  - https://doi.org/10.1002/ece3.5878
SN  - 2045-7758
VL  - 9
IS  - 24
SP  - 14430
EP  - 14441
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Eilers, Elisabeth Johanna
A1  - Heger, Tina
T1  - Past Competition Affects Offspring Foliar Terpenoid Concentrations, Seed Traits, and Fitness in the Invasive Forb Erodium cicutarium (Geraniaceae)
JF  - Frontiers in Ecology and Evolution
N2  - (1) Environmental conditions experienced in the past may lead to intraspecific differences in ecological and chemical traits of plants, which likely affect future responses to altered or new environments. Whether competition by neighbors is such a trait-shaping factor is not yet well-known. We aimed to understand how the level of ancestral plant competition affects traits related to plant fitness and resource allocation, reproduction, and (phyto-)toxin accumulation in offspring, and whether a potential differentiation in these traits can be found in different geographic origins of which one belongs to the native and one to the invaded range. (2) We compared differentiation of the following traits in offspring plants of multiple populations in Erodium cicutarium (Geraniaceae): biomass, seed production, seed traits related to dispersal and germination, and concentrations of foliar mono- and sesquiterpenes. We tested the allelopatic potential of aqueous extracts of the same E. cicutarium plants on seeds of five different plant families. (3) In plants originating from populations that experienced high levels of competition, we found twice as high monoterpene concentrations. These plants also produced more biomass and a higher proportion of ripe to unripe seeds until harvesting. Seeds originating from high competition sites were shorter. Aqueous E. cicutarium leaf extracts with high terpenoid content reduced radicle length of Zea mays and radicle and hypocotyl length of E. cicutarium seedlings. (4) The results of this study provide first evidence that the surrounding vegetation may shape chemo-ecological plant traits that may be fundamental for competitive ability. Our study calls for more research testing whether competition experienced in the native range may lead to an enhanced capability of plants to establish populations and spread in a new range.
KW  - resource allocation
KW  - specialized metabolites
KW  - gas chromatography-mass spectrometry
KW  - seed morphology
KW  - plant interactions
KW  - eco-evolutionary experience
Y1  - 2019
U6  - https://doi.org/10.3389/fevo.2019.00392
SN  - 2296-701X
VL  - 7
PB  - Frontiers Research Foundation
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Paragas, Erickson M.
A1  - Humphreys, Sara C.
A1  - Min, Joshua
A1  - Joswig-Jones, Carolyn A.
A1  - Leimkühler, Silke
A1  - Jones, Jeffrey P.
T1  - ecoAO
BT  - a simple system for the study of human aldehyde oxidases role in drug metabolism
JF  - ACS OMEGA
N2  - Although aldehyde oxidase (AO) is an important hepatic drug-metabolizing enzyme, it remains understudied and is consequently often overlooked in preclinical studies, an oversight that has resulted in the failure of multiple clinical trials. AO’s preclusion to investigation stems from the following: (1) difficulties synthesizing metabolic standards due to the chemospecificity and regiospecificity of the enzyme and (2) significant inherent variability across existing in vitro systems including liver cytosol, S9 fractions, and primary hepatocytes, which lack specificity and generate discordant expression and activity profiles. Here, we describe a practical bacterial biotransformation system, ecoAO, addressing both issues simultaneously. ecoAO is a cell paste of MoCo-producing Escherichia coli strain TP1017 expressing human AO. It exhibits specific activity toward known substrates, zoniporide, 4-trans-(N,N-dimethylamino)cinnamaldehyde, O6-benzylguanine, and zaleplon; it also has utility as a biocatalyst, yielding milligram quantities of synthetically challenging metabolite standards such as 2-oxo-zoniporide. Moreover, ecoAO enables routine determination of kcat and V/K, which are essential parameters for accurate in vivo clearance predictions. Furthermore, ecoAO has potential as a preclinical in vitro screening tool for AO activity, as demonstrated by its metabolism of 3-aminoquinoline, a previously uncharacterized substrate. ecoAO promises to provide easy access to metabolites with the potential to improve pharmacokinetic clearance predictions and guide drug development.
Y1  - 2017
U6  - https://doi.org/10.1021/acsomega.7b01054
SN  - 2470-1343
VL  - 2
SP  - 4820
EP  - 4827
PB  - American Chemical Society
CY  - Washington
ER  - 
TY  - JOUR
A1  - Lukan, Tjaša
A1  - Machens, Fabian
A1  - Coll, Anna
A1  - Baebler, Špela
A1  - Messerschmidt, Katrin
A1  - Gruden, Kristina
T1  - Plant X-tender
BT  - an extension of the AssemblX system for the assembly and expression of multigene constructs in plants
JF  - PLOS ONE
N2  - Cloning multiple DNA fragments for delivery of several genes of interest into the plant genome is one of the main technological challenges in plant synthetic biology. Despite several modular assembly methods developed in recent years, the plant biotechnology community has not widely adopted them yet, probably due to the lack of appropriate vectors and software tools. Here we present Plant X-tender, an extension of the highly efficient, scar-free and sequence-independent multigene assembly strategy AssemblX, based on overlap-depended cloning methods and rare-cutting restriction enzymes. Plant X-tender consists of a set of plant expression vectors and the protocols for most efficient cloning into the novel vector set needed for plant expression and thus introduces advantages of AssemblX into plant synthetic biology. The novel vector set covers different backbones and selection markers to allow full design flexibility. We have included ccdB counterselection, thereby allowing the transfer of multigene constructs into the novel vector set in a straightforward and highly efficient way. Vectors are available as empty backbones and are fully flexible regarding the orientation of expression cassettes and addition of linkers between them, if required. We optimised the assembly and subcloning protocol by testing different scar-less assembly approaches: the noncommercial SLiCE and TAR methods and the commercial Gibson assembly and NEBuilder HiFi DNA assembly kits. Plant X-tender was applicable even in combination with low efficient homemade chemically competent or electrocompetent Escherichia coli. We have further validated the developed procedure for plant protein expression by cloning two cassettes into the newly developed vectors and subsequently transferred them to Nicotiana benthamiana in a transient expression setup. Thereby we show that multigene constructs can be delivered into plant cells in a streamlined and highly efficient way. Our results will support faster introduction of synthetic biology into plant science.
Y1  - 2018
U6  - https://doi.org/10.1371/journal.pone.0190526
SN  - 1932-6203
VL  - 13
IS  - 1
PB  - Public Library of Science
CY  - San Fransisco
ER  - 
TY  - JOUR
A1  - Busch, Verena
A1  - Klaus, Valentin H.
A1  - Penone, Caterina
A1  - Schäfer, Deborah
A1  - Boch, Steffen
A1  - Prati, Daniel
A1  - Müller, Jörg
A1  - Socher, Stephanie A.
A1  - Niinemets, Ülo
A1  - Penuelas, Josep
A1  - Hölzel, Norbert
A1  - Fischer, Markus
A1  - Kleinebecker, Till
T1  - Nutrient stoichiometry and land use rather than species richness determine plant functional diversity
JF  - Ecology and evolution
N2  - Plant functional traits reflect individual and community ecological strategies. They allow the detection of directional changes in community dynamics and ecosystemic processes, being an additional tool to assess biodiversity than species richness. Analysis of functional patterns in plant communities provides mechanistic insight into biodiversity alterations due to anthropogenic activity. Although studies have consi-dered of either anthropogenic management or nutrient availability on functional traits in temperate grasslands, studies combining effects of both drivers are scarce. Here, we assessed the impacts of management intensity (fertilization, mowing, grazing), nutrient stoichiometry (C, N, P, K), and vegetation composition on community-weighted means (CWMs) and functional diversity (Rao's Q) from seven plant traits in 150 grasslands in three regions in Germany, using data of 6 years. Land use and nutrient stoichiometry accounted for larger proportions of model variance of CWM and Rao's Q than species richness and productivity. Grazing affected all analyzed trait groups; fertilization and mowing only impacted generative traits. Grazing was clearly associated with nutrient retention strategies, that is, investing in durable structures and production of fewer, less variable seed. Phenological variability was increased. Fertilization and mowing decreased seed number/mass variability, indicating competition-related effects. Impacts of nutrient stoichiometry on trait syndromes varied. Nutrient limitation (large N:P, C:N ratios) promoted species with conservative strategies, that is, investment in durable plant structures rather than fast growth, fewer seed, and delayed flowering onset. In contrast to seed mass, leaf-economics variability was reduced under P shortage. Species diversity was positively associated with the variability of generative traits. Synthesis. Here, land use, nutrient availability, species richness, and plant functional strategies have been shown to interact complexly, driving community composition, and vegetation responses to management intensity. We suggest that deeper understanding of underlying mechanisms shaping community assembly and biodiversity will require analyzing all these parameters.
KW  - biodiversity exploratories
KW  - fertilization
KW  - leaf economics
KW  - mowing
KW  - nutrient availability
KW  - nutrient ratios
KW  - phosphorus
KW  - plant functional traits
KW  - plant strategies
KW  - seed mass
Y1  - 2017
U6  - https://doi.org/10.1002/ece3.3609
SN  - 2045-7758
VL  - 8
IS  - 1
SP  - 601
EP  - 616
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Reinhardt, Julia
A1  - Liersch, Stefan
A1  - Abdeladhim, Mohamed Arbi
A1  - Diallo, Mori
A1  - Dickens, Chris
A1  - Fournet, Samuel
A1  - Hattermann, Fred Fokko
A1  - Kabaseke, Clovis
A1  - Muhumuza, Moses
A1  - Mul, Marloes L.
A1  - Pilz, Tobias
A1  - Otto, Ilona M.
A1  - Walz, Ariane
T1  - Systematic evaluation of scenario assessments supporting sustainable integrated natural resources management
BT  - evidence from four case studies in Africa
JF  - Ecology and society : a journal of integrative science for resilience and sustainability
N2  - Scenarios have become a key tool for supporting sustainability research on regional and global change. In this study we evaluate four regional scenario assessments: first, to explore a number of research challenges related to sustainability science and, second, to contribute to sustainability research in the specific case studies. The four case studies used commonly applied scenario approaches that are (i) a story and simulation approach with stakeholder participation in the Oum Zessar watershed, Tunisia, (ii) a participatory scenario exploration in the Rwenzori region, Uganda, (iii) a model-based prepolicy study in the Inner Niger Delta, Mali, and (iv) a model coupling-based scenario analysis in upper Thukela basin, South Africa. The scenario assessments are evaluated against a set of known challenges in sustainability science, with each challenge represented by two indicators, complemented by a survey carried out on the perception of the scenario assessments within the case study regions. The results show that all types of scenario assessments address many sustainability challenges, but that the more complex ones based on story and simulation and model coupling are the most comprehensive. The study highlights the need to investigate abrupt system changes as well as governmental and political factors as important sources of uncertainty. For an in-depth analysis of these issues, the use of qualitative approaches and an active engagement of local stakeholders are suggested. Studying ecological thresholds for the regional scale is recommended to support research on regional sustainability. The evaluation of the scenario processes and outcomes by local researchers indicates the most transparent scenario assessments as the most useful. Focused, straightforward, yet iterative scenario assessments can be very relevant by contributing information to selected sustainability problems.
KW  - Africa
KW  - global and regional change
KW  - integrated assessments
KW  - participatory research
KW  - sustainability science
Y1  - 2018
U6  - https://doi.org/10.5751/ES-09728-230105
SN  - 1708-3087
VL  - 23
IS  - 1
PB  - Resilience Alliance
CY  - Wolfville
ER  - 
TY  - JOUR
A1  - Kolora, Sree Rohit Raj
A1  - Weigert, Anne
A1  - Saffari, Amin
A1  - Kehr, Stephanie
A1  - Walter Costa, Maria Beatriz
A1  - Spröer, Cathrin
A1  - Indrischek, Henrike
A1  - Chintalapati, Manjusha
A1  - Lohse, Konrad
A1  - Doose, Gero
A1  - Overmann, Jörg
A1  - Bunk, Boyke
A1  - Bleidorn, Christoph
A1  - Grimm-Seyfarth, Annegret
A1  - Henle, Klaus
A1  - Nowick, Katja
A1  - Faria, Rui
A1  - Stadler, Peter F.
A1  - Schlegel, Martin
T1  - Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation
JF  - GigaScience
N2  - Background Lacerta viridis and Lacerta bilineata are sister species of European green lizards (eastern and western clades, respectively) that, until recently, were grouped together as the L. viridis complex. Genetic incompatibilities were observed between lacertid populations through crossing experiments, which led to the delineation of two separate species within the L. viridis complex. The population history of these sister species and processes driving divergence are unknown. We constructed the first high-quality de novo genome assemblies for both L. viridis and L. bilineata through Illumina and PacBio sequencing, with annotation support provided from transcriptome sequencing of several tissues. To estimate gene flow between the two species and identify factors involved in reproductive isolation, we studied their evolutionary history, identified genomic rearrangements, detected signatures of selection on non-coding RNA, and on protein-coding genes. Findings Here we show that gene flow was primarily unidirectional from L. bilineata to L. viridis after their split at least 1.15 million years ago. We detected positive selection of the non-coding repertoire; mutations in transcription factors; accumulation of divergence through inversions; selection on genes involved in neural development, reproduction, and behavior, as well as in ultraviolet-response, possibly driven by sexual selection, whose contribution to reproductive isolation between these lacertid species needs to be further evaluated. Conclusion The combination of short and long sequence reads resulted in one of the most complete lizard genome assemblies. The characterization of a diverse array of genomic features provided valuable insights into the demographic history of divergence among European green lizards, as well as key species differences, some of which are candidates that could have played a role in speciation. In addition, our study generated valuable genomic resources that can be used to address conservation-related issues in lacertids.
KW  - sister species
KW  - PacBio and Illumina
KW  - de novo hybrid assembly
KW  - transcripts
KW  - noncoding RNA
KW  - zinc fingers
KW  - positive selection
KW  - UV response
KW  - inversions
KW  - gene flow
Y1  - 2018
U6  - https://doi.org/10.1093/gigascience/giy160
SN  - 2047-217X
VL  - 8
IS  - 2
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Sowemimo, Oluwakemi T.
A1  - Knox-Brown, Patrick
A1  - Borcherds, Wade
A1  - Rindfleisch, Tobias
A1  - Thalhammer, Anja
A1  - Daughdrill, Gary W.
T1  - Conserved Glycines Control Disorder and Function in the Cold-Regulated Protein, COR15A
JF  - Biomolecules
N2  - Cold-regulated (COR) 15A is an intrinsically disordered protein (IDP) from Arabidopsis thaliana important for freezing tolerance. During freezing-induced cellular dehydration, COR15A transitions from a disordered to mostly alpha-helical structure. We tested whether mutations that increase the helicity of COR15A also increase its protective function. Conserved glycine residues were identified and mutated to alanine. Nuclear magnetic resonance (NMR) spectroscopy was used to identify residue-specific changes in helicity for wildtype (WT) COR15A and the mutants. Circular dichroism (CD) spectroscopy was used to monitor the coil-helix transition in response to increasing concentrations of trifluoroethanol (TFE) and ethylene glycol. The impact of the COR15A mutants on the stability of model membranes during a freeze-thaw cycle was investigated by fluorescence spectroscopy. The results of these experiments showed the mutants had a higher content of alpha-helical structure and the increased alpha-helicity improved membrane stabilization during freezing. Comparison of the TFE- and ethylene glycol-induced coil-helix transitions support our conclusion that increasing the transient helicity of COR15A in aqueous solution increases its ability to stabilize membranes during freezing. Altogether, our results suggest the conserved glycine residues are important for maintaining the disordered structure of COR15A but are also compatible with the formation of alpha-helical structure during freezing induced dehydration.
KW  - COR15A
KW  - Late embryogenesis abundant
KW  - intrinsically disordered proteins
KW  - Trifluoroethanol
KW  - Nuclear magnetic resonance
Y1  - 2019
U6  - https://doi.org/10.3390/biom9030084
SN  - 2218-273X
VL  - 9
IS  - 3
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Bubner, Ben
A1  - Buchheit, Ramona
A1  - Friedrich, Frank
A1  - Kummer, Volker
A1  - Scholler, Markus
T1  - Species identification of European forest pathogens of the genus Milesina (Pucciniales) using urediniospore morphology and molecular barcoding including M. woodwardiana sp. nov.
JF  - MycoKeys
N2  - Species of rust fungi of the genus Milesina (Pucciiastraceae, Pucciniales) are distributed mainly in northern temperate regions. They host-alternate between needles of fir (Abies spp.) and fronds of ferns (species of Polypodiales). Milesina species are distinguished based on host taxonomy and urediniospore morphology. In this study, 12 species of Milesina from Europe were revised. Specimens were examined by light and scanning electron microscopy for urediniospore morphology with a focus on visualising germ pores (number, size and position) and echinulation. In addition, barcode loci (ITS, nad6, 28S) were used for species delimitation and for molecular phylogenetic analyses. Barcodes of 72 Milesina specimens were provided, including 11 of the 12 species. Whereas urediniospore morphology features were sufficient to distinguish all 12 Milesina species except for 2 (M. blechni and M. kriegeriana), ITS sequences separated only 4 of 11 species. Sequencing with 28S and nad6 did not improve species resolution. Phylogenetic analysis, however, revealed four phylogenetic groups within Milesina that also correlate with specific urediniospore characters (germ pore number and position and echinulation). These groups are proposed as new sections within Milesina (sections Milesina, Vogesiacae M. Scholler & Bubner, sect. nov., Scolopendriorum M. Scholler & Bubner, sect. nov. and Carpaticae M. Scholler & Bubner, sect. nov.). In addition, Milesina woodwardiana Buchheit & M. Scholler, sp. nov. on Woodwardia radicans, a member of the type section Milesina, is newly described. An identification key for European Milesina species, based on urediniospore features, is provided.
KW  - Abies alba
KW  - Polypodiales
KW  - GBOL
KW  - germ pores
KW  - host alternation
KW  - Uredinopsis
KW  - Europe
Y1  - 2019
U6  - https://doi.org/10.3897/mycokeys.48.30350
SN  - 1314-4057
SN  - 1314-4049
IS  - 48
SP  - 1
EP  - 40
PB  - Pensoft Publishers
CY  - Sofia
ER  - 
TY  - JOUR
A1  - Heinrichs, Steffi
A1  - Ammer, Christian
A1  - Mund, Martina
A1  - Boch, Steffen
A1  - Budde, Sabine
A1  - Fischer, Markus
A1  - Mueller, Joerg
A1  - Schoening, Ingo
A1  - Schulze, Ernst-Detlef
A1  - Schmidt, Wolfgang
A1  - Weckesser, Martin
A1  - Schall, Peter
T1  - Landscape-Scale Mixtures of Tree Species are More Effective than Stand-Scale Mixtures for Biodiversity of Vascular Plants, Bryophytes and Lichens
JF  - Forests
N2  - Tree species diversity can positively affect the multifunctionality of forests. This is why conifer monocultures of Scots pine and Norway spruce, widely promoted in Central Europe since the 18th and 19th century, are currently converted into mixed stands with naturally dominant European beech. Biodiversity is expected to benefit from these mixtures compared to pure conifer stands due to increased abiotic and biotic resource heterogeneity. Evidence for this assumption is, however, largely lacking. Here, we investigated the diversity of vascular plants, bryophytes and lichens at the plot (alpha diversity) and at the landscape (gamma diversity) level in pure and mixed stands of European beech and conifer species (Scots pine, Norway spruce, Douglas fir) in four regions in Germany. We aimed to identify compositions of pure and mixed stands in a hypothetical forest landscape that can optimize gamma diversity of vascular plants, bryophytes and lichens within regions. Results show that gamma diversity of the investigated groups is highest when a landscape comprises different pure stands rather than tree species mixtures at the stand scale. Species mainly associated with conifers rely on light regimes that are only provided in pure conifer forests, whereas mixtures of beech and conifers are more similar to beech stands. Combining pure beech and pure conifer stands at the landscape scale can increase landscape level biodiversity and conserve species assemblages of both stand types, while landscapes solely composed of stand scale tree species mixtures could lead to a biodiversity reduction of a combination of investigated groups of 7 up to 20%.
KW  - Fagus sylvatica
KW  - Pinus sylvestris
KW  - Picea abies
KW  - Pseudotsuga menziesii
KW  - forest management
KW  - tree species diversity
KW  - forest conversion
KW  - gamma diversity
KW  - landscape scale
KW  - Biodiversity Exploratories
Y1  - 2019
U6  - https://doi.org/10.3390/f10010073
SN  - 1999-4907
VL  - 10
IS  - 1
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Mota, Cristiano
A1  - Esmaeeli Moghaddam Tabalvandani, Mariam
A1  - Coelho, Catarina
A1  - Santos-Silva, Teresa
A1  - Wolff, Martin
A1  - Foti, Alessandro
A1  - Leimkühler, Silke
A1  - Romao, Maria Joao
T1  - Human aldehyde oxidase (hAOX1)
BT  - structure determination of the Moco-free form of the natural variant G1269R and biophysical studies of single nucleotide polymorphisms
JF  - FEBS Open Bio
N2  - Human aldehyde oxidase (hAOX1) is a molybdenum enzyme with high toxicological importance, but its physiological role is still unknown. hAOX1 metabolizes different classes of xenobiotics and is one of the main drug-metabolizing enzymes in the liver, along with cytochrome P450. hAOX1 oxidizes and inactivates a large number of drug molecules and has been responsible for the failure of several phase I clinical trials. The interindividual variability of drug-metabolizing enzymes caused by single nucleotide polymorphisms (SNPs) is highly relevant in pharmaceutical treatments. In this study, we present the crystal structure of the inactive variant G1269R, revealing the first structure of a molybdenum cofactor (Moco)-free form of hAOX1. These data allowed to model, for the first time, the flexible Gate 1 that controls access to the active site. Furthermore, we inspected the thermostability of wild-type hAOX1 and hAOX1 with various SNPs (L438V, R1231H, G1269R or S1271L) by CD spectroscopy and ThermoFAD, revealing that amino acid exchanges close to the Moco site can impact protein stability up to 10 degrees C. These results correlated with biochemical and structural data and enhance our understanding of hAOX1 and the effect of SNPs in the gene encoding this enzyme in the human population. EnzymesAldehyde oxidase (); xanthine dehydrogenase (); xanthine oxidase (). DatabasesStructural data are available in the Protein Data Bank under the accession number .
KW  - human aldehyde oxidase
KW  - molybdenum cofactor
KW  - single nucleotide polymorphism
KW  - xanthine oxidase
Y1  - 2019
U6  - https://doi.org/10.1002/2211-5463.12617
SN  - 2211-5463
VL  - 9
IS  - 5
SP  - 925
EP  - 934
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Sroka, Pavel
A1  - Godunko, Roman J.
A1  - Rutschmann, Sereina
A1  - Angeli, Kamila B.
A1  - Salles, Frederico F.
A1  - Gattolliat, Jean-Luc
T1  - A new species of Bungona in Turkey (Ephemeroptera, Baetidae)
BT  - an unexpected biogeographic pattern within a pantropical complex of mayflies
JF  - Zoosytematics and evolution
N2  - By using an integrative approach, we describe a new species of mayfly, Bungona (Chopralla) pontica sp. n., from Turkey. The discovery of a representative of the tropical mayfly genus Bungona in the Middle East is rather unexpected. The new species shows all the main morphological characters of the subgenus Chopralla, which has its closest related species occurring in southeastern Asia. Barcoding clearly indicated that the new species represents an independent lineage isolated for a very long time from other members of the complex. The claw is equipped with two rows of three or four flattened denticles. This condition is a unique feature of Bungona (Chopralla) pontica sp. n. among West Palaearctic mayfly species. Within the subgenus Chopralla, the species can be identified by the presence of a simple, not bifid right prostheca (also present only in Bungona (Chopralla) liebenauae (Soldan, Braasch & Muu, 1987)), the shape of the labial palp, and the absence of protuberances on pronotum.
KW  - Biogeography
KW  - Cloeodes complex
KW  - Chopralla
KW  - integrative taxonomy
KW  - Middle East
KW  - new species
Y1  - 2019
U6  - https://doi.org/10.3897/zse.95.29487
SN  - 1860-0743
VL  - 95
IS  - 1
SP  - 1
EP  - 13
PB  - Pensoft Publ.
CY  - Sofia
ER  - 
TY  - JOUR
A1  - Kurbanoglu, Sevinc
A1  - Yarman, Aysu
T1  - Simultaneous determination of hydrochlorothiazide and irbesartan from pharmaceutical dosage forms with RP-HPLC
T1  - Farmasötik Dozaj Formlarında TF-YPSK ile Hidroklorotiyazid ve
İrbesartanın Eş Zamanlı Tayini
JF  - Turkish journal of pharmaceutical sciences
N2  - Objectives: In this work, a simple and rapid liquid chromatographic method for the simultaneous determination of irbesartan (IRBE) and hydrochlorothiazide (HCT) was developed and validated by reverse phase high performance liquid chromatography (RP-HPLC). <br /> Materials and Methods: Experimental conditions such as different buffer solutions, various pH values, temperature, composition of the mobile phase, and the effect of flow rate were optimized. <br /> Results: The developed RP-HPLC method for these antihypertensive agents was wholly validated and IRBE was detected in the linear range of 0.1-25 mu g mL(-1) and HCT was detected in the linear range of 0.25-25 mu g mL(-1). Moreover, the suggested chromatographic technique was successfully applied for the determination of the drugs in human serum and pharmaceutical dosage forms with limit of detection values of 0.008 mu g mL(-1) for IRBE and 0.012 mu g mL(-1) for HCT. <br /> Conclusion: The proposed rapid analysis method of these antihypertensive drugs can be easily used and applied by pharmaceutical companies for which the analysis time is important.
N2  - Amaç: Bu çalışmada, irbesartan (IRBE) ve hidroklorotiyazidin (HCT) eşzamanlı tayini için basit ve hızlı bir ters fazlı yüksek performanslı sıvı
kromatografisi (TF-YPSK) yöntemi geliştirilmiş ve validasyon çalışmaları yapılmıştır.
Gereç ve Yöntemler: Deneysel koşullar; farklı tampon çözeltileri, çeşitli pH değerleri, sıcaklık, mobil fazın bileşimi, akış hızının etkisi gibi
parametrelerin üzerinden optimize edildi.
Bulgular: Bu antihipertansif ajanlar için geliştirilen TF-YPSK yönteminin tüm validasyon parametrelerine ilişkin çalışmalar yapılmış, ve IRBE 0,1-25
μg mL-1 doğrusal aralığında ve HCT 0,25-25 μg mL-1 doğrusal aralığında tespit edilmiştir. Ayrıca önerilen TF-YPSK yöntemi ile IRBE için 0,008 μg
mL-1 ve HCT için 0,012 μg mL-1 tayin alt sınır değerleri bulunmuştur. Geliştirilen yöntem, insan serumunda ve farmasötik dozaj formlarında bulunan
IRBE ve HCT’nin belirlenmesi için başarıyla uygulanmıştır.
Sonuç: Bu antihipertansif ilaçların miktar tayininde önerilen YPSK analiz yönteminin, analiz süresinin önemli olduğu ilaç firmalarında rahatlıkla
kullanılabileceği ve uygulanabileceği düşünülmektedir.
KW  - HPLC
KW  - irbesartan
KW  - hydrochlorothiazide
KW  - pharmaceutical dosage forms
Y1  - 2020
U6  - https://doi.org/10.4274/tjps.galenos.2019.76094
SN  - 1304-530X
VL  - 17
IS  - 5
SP  - 523
EP  - 527
PB  - Turkish Pharmacists Association
CY  - Çankaya-Ankara
ER  -