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  - 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  - 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  -