TY  - JOUR
A1  - Wiesner-Reinhold, Melanie
A1  - Barknowitz, Gitte
A1  - Florian, Simone
A1  - Mewis, Inga
A1  - Schumacher, Fabian
A1  - Schreiner, Monika
A1  - Glatt, Hansruedi
T1  - 1-Methoxy-3-indolylmethyl DNA adducts in six tissues, and blood protein adducts, in mice under pak choi diet: time course and persistence
JF  - Archives of toxicology : official journal of EUROTOX
N2  - We previously showed that purified 1-methoxy-3-indolylmethyl (1-MIM) glucosinolate, a secondary plant metabolite in Brassica species, is mutagenic in various in vitro systems and forms DNA and protein adducts in mouse models. In the present study, we administered 1-MIM glucosinolate in a natural matrix to mice, by feeding a diet containing pak choi powder and extract. Groups of animals were killed after 1, 2, 4 and 8 days of pak choi diet, directly or, in the case of the 8-day treatment, after 0, 8 and 16 days of recovery with pak choi-free diet. DNA adducts [N-2-(1-MIM)-dG, N-6-(1-MIM)-dA] in six tissues, as well as protein adducts [tau N-(1-MIM)-His] in serum albumin (SA) and hemoglobin (Hb) were determined using UPLC-MS/MS with isotopically labeled internal standards. None of the samples from the 12 control animals under standard diet contained any 1-MIM adducts. All groups receiving pak choi diet showed DNA adducts in all six tissues (exception: lung of mice treated for a single day) as well as SA and Hb adducts. During the feeding period, all adduct levels continuously increased until day 8 (in the jejunum until day 4). During the 14-day recovery period, N-2-(1-MIM)-dG in liver, kidney, lung, jejunum, cecum and colon decreased to 52, 41, 59, 11, 7 and 2%, respectively, of the peak level. The time course of N-6-(1-MIM)-dA was similar. Immunohistochemical analyses indicated that cell turnover is a major mechanism of DNA adduct elimination in the intestine. In the same recovery period, protein adducts decreased more rapidly in SA than in Hb, to 0.7 and 37%, respectively, of the peak level, consistent with the differential turnover of these proteins. In conclusion, the pak choi diet lead to the formation of high levels of adducts in mice. Cell and protein turnover was a major mechanism of adduct elimination, at least in gut and blood.
KW  - 1-Methoxy-3-indolylmethyl glucosinolate
KW  - Neoglucobrassicin
KW  - DNA adducts
KW  - Blood protein adducts
KW  - Pak choi
Y1  - 2019
U6  - https://doi.org/10.1007/s00204-019-02452-3
SN  - 0340-5761
SN  - 1432-0738
VL  - 93
IS  - 6
SP  - 1515
EP  - 1527
PB  - Springer
CY  - Heidelberg
ER  - 
TY  - THES
A1  - Bendadani, Carolin
T1  - 1-Methylpyren: Biotransformation und Gentoxizität
Y1  - 2015
ER  - 
TY  - THES
A1  - Balk, Maria
T1  - 3D structured shape-memory hydrogels with enzymatically-induced shape shifting
Y1  - 2015
ER  - 
TY  - JOUR
A1  - Leong, Jia Xuan
A1  - Raffeiner, Margot
A1  - Spinti, Daniela
A1  - Langin, Gautier
A1  - Franz-Wachtel, Mirita
A1  - Guzman, Andrew R.
A1  - Kim, Jung-Gun
A1  - Pandey, Pooja
A1  - Minina, Alyona E.
A1  - Macek, Boris
A1  - Hafren, Anders
A1  - Bozkurt, Tolga O.
A1  - Mudgett, Mary Beth
A1  - Börnke, Frederik
A1  - Hofius, Daniel
A1  - Uestuen, Suayib
T1  - A bacterial effector counteracts host autophagy by promoting degradation of an autophagy component
JF  - The EMBO journal
N2  - Beyond its role in cellular homeostasis, autophagy plays anti- and promicrobial roles in host-microbe interactions, both in animals and plants. 
One prominent role of antimicrobial autophagy is to degrade intracellular pathogens or microbial molecules, in a process termed xenophagy. 
Consequently, microbes evolved mechanisms to hijack or modulate autophagy to escape elimination. 
Although well-described in animals, the extent to which xenophagy contributes to plant-bacteria interactions remains unknown. 

Here, we provide evidence that Xanthomonas campestris pv. vesicatoria (Xcv) suppresses host autophagy by utilizing type-III effector XopL. XopL interacts with and degrades the autophagy component SH3P2 via its E3 ligase activity to promote infection. 
Intriguingly, XopL is targeted for degradation by defense-related selective autophagy mediated by NBR1/Joka2, revealing a complex antagonistic interplay between XopL and the host autophagy machinery. 

Our results implicate plant antimicrobial autophagy in the depletion of a bacterial virulence factor and unravel an unprecedented pathogen strategy to counteract defense-related autophagy in plant-bacteria interactions.
KW  - autophagy
KW  - effectors
KW  - immunity
KW  - ubiquitination
KW  - xenophagy
Y1  - 2022
U6  - https://doi.org/10.15252/embj.2021110352
SN  - 1460-2075
VL  - 41
IS  - 13
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - GEN
A1  - Balazadeh, Salma
A1  - Müller-Röber, Bernd
T1  - A balance to death
T2  - Nature plants
N2  - Leaf senescence plays a crucial role in nutrient recovery in late-stage plant development and requires vast transcriptional reprogramming by transcription factors such as ORESARA1 (ORE1). A proteolytic mechanism is now found to control ORE1 degradation, and thus senescence, during nitrogen starvation.
Y1  - 2018
U6  - https://doi.org/10.1038/s41477-018-0279-6
SN  - 2055-026X
SN  - 2055-0278
VL  - 4
IS  - 11
SP  - 863
EP  - 864
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Klauschies, Toni
A1  - Coutinho, Renato Mendes
A1  - Gaedke, Ursula
T1  - A beta distribution-based moment closure enhances the reliability of trait-based aggregate models for natural populations and communities
JF  - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog
N2  - Ecological communities are complex adaptive systems that exhibit remarkable feedbacks between their biomass and trait dynamics. Trait-based aggregate models cope with this complexity by focusing on the temporal development of the community’s aggregate properties such as its total biomass, mean trait and trait variance. They are based on particular assumptions about the shape of the underlying trait distribution, which is commonly assumed to be normal. However, ecologically important traits are usually restricted to a finite range, and empirical trait distributions are often skewed or multimodal. As a result, normal distribution-based aggregate models may fail to adequately represent the biomass and trait dynamics of natural communities. We resolve this mismatch by developing a new moment closure approach assuming the trait values to be beta-distributed. We show that the beta distribution captures important shape properties of both observed and simulated trait distributions, which cannot be captured by a Gaussian. We further demonstrate that a beta distribution-based moment closure can strongly enhance the reliability of trait-based aggregate models. We compare the biomass, mean trait and variance dynamics of a full trait distribution (FD) model to the ones of beta (BA) and normal (NA) distribution-based aggregate models, under different selection regimes. This way, we demonstrate under which general conditions (stabilizing, fluctuating or disruptive selection) different aggregate models are reliable tools. All three models predicted very similar biomass and trait dynamics under stabilizing selection yielding unimodal trait distributions with small standing trait variation. We also obtained an almost perfect match between the results of the FD and BA models under fluctuating selection, promoting skewed trait distributions and ongoing oscillations in the biomass and trait dynamics. In contrast, the NA model showed unrealistic trait dynamics and exhibited different alternative stable states, and thus a high sensitivity to initial conditions under fluctuating selection. Under disruptive selection, both aggregate models failed to reproduce the results of the FD model with the mean trait values remaining within their ecologically feasible ranges in the BA model but not in the NA model. Overall, a beta distribution-based moment closure strongly improved the realism of trait-based aggregate models.
KW  - Moment closure
KW  - Normal and beta distribution
KW  - Skewed and peaked trait distributions
KW  - Fitness landscape and frequency-dependent selection
KW  - Eco-evolutionary dynamics
KW  - Modelling functional diversity
Y1  - 2018
U6  - https://doi.org/10.1016/j.ecolmodel.2018.02.001
SN  - 0304-3800
SN  - 1872-7026
VL  - 381
SP  - 46
EP  - 77
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - GEN
A1  - Omidbakhshfard, Mohammad Amin
A1  - Neerakkal, Sujeeth
A1  - Gupta, Saurabh
A1  - Omranian, Nooshin
A1  - Guinan, Kieran J.
A1  - Brotman, Yariv
A1  - Nikoloski, Zoran
A1  - Fernie, Alisdair R.
A1  - Mueller-Roeber, Bernd
A1  - Gechev, Tsanko S.
T1  - A Biostimulant Obtained from the Seaweed Ascophyllum nodosum Protects Arabidopsis thaliana from Severe Oxidative Stress
T2  - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe
N2  - Abiotic stresses cause oxidative damage in plants. Here, we demonstrate that foliar application of an extract from the seaweed Ascophyllum nodosum, SuperFifty (SF), largely prevents paraquat (PQ)-induced oxidative stress in Arabidopsis thaliana. While PQ-stressed plants develop necrotic lesions, plants pre-treated with SF (i.e., primed plants) were unaffected by PQ. Transcriptome analysis revealed induction of reactive oxygen species (ROS) marker genes, genes involved in ROS-induced programmed cell death, and autophagy-related genes after PQ treatment. These changes did not occur in PQ-stressed plants primed with SF. In contrast, upregulation of several carbohydrate metabolism genes, growth, and hormone signaling as well as antioxidant-related genes were specific to SF-primed plants. Metabolomic analyses revealed accumulation of the stress-protective metabolite maltose and the tricarboxylic acid cycle intermediates fumarate and malate in SF-primed plants. Lipidome analysis indicated that those lipids associated with oxidative stress-induced cell death and chloroplast degradation, such as triacylglycerols (TAGs), declined upon SF priming. Our study demonstrated that SF confers tolerance to PQ-induced oxidative stress in A. thaliana, an effect achieved by modulating a range of processes at the transcriptomic, metabolic, and lipid levels.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 823 
KW  - Ascophyllum nodosum
KW  - Arabidopsis thaliana
KW  - biostimulant
KW  - paraquat
KW  - priming
KW  - oxidative stress tolerance
KW  - reactive oxygen species
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-445093
SN  - 1866-8372
IS  - 823
ER  - 
TY  - JOUR
A1  - Omidbakhshfard, Mohammad Amin
A1  - Neerakkal, Sujeeth
A1  - Gupta, Saurabh
A1  - Omranian, Nooshin
A1  - Guinan, Kieran J.
A1  - Brotman, Yariv
A1  - Nikoloski, Zoran
A1  - Fernie, Alisdair R.
A1  - Mueller-Roeber, Bernd
A1  - Gechev, Tsanko S.
T1  - A Biostimulant Obtained from the Seaweed Ascophyllum nodosum Protects Arabidopsis thaliana from Severe Oxidative Stress
JF  - International Journal of Molecular Sciences
N2  - Abiotic stresses cause oxidative damage in plants. Here, we demonstrate that foliar application of an extract from the seaweed Ascophyllum nodosum, SuperFifty (SF), largely prevents paraquat (PQ)-induced oxidative stress in Arabidopsis thaliana. While PQ-stressed plants develop necrotic lesions, plants pre-treated with SF (i.e., primed plants) were unaffected by PQ. Transcriptome analysis revealed induction of reactive oxygen species (ROS) marker genes, genes involved in ROS-induced programmed cell death, and autophagy-related genes after PQ treatment. These changes did not occur in PQ-stressed plants primed with SF. In contrast, upregulation of several carbohydrate metabolism genes, growth, and hormone signaling as well as antioxidant-related genes were specific to SF-primed plants. Metabolomic analyses revealed accumulation of the stress-protective metabolite maltose and the tricarboxylic acid cycle intermediates fumarate and malate in SF-primed plants. Lipidome analysis indicated that those lipids associated with oxidative stress-induced cell death and chloroplast degradation, such as triacylglycerols (TAGs), declined upon SF priming. Our study demonstrated that SF confers tolerance to PQ-induced oxidative stress in A. thaliana, an effect achieved by modulating a range of processes at the transcriptomic, metabolic, and lipid levels.
KW  - Ascophyllum nodosum
KW  - Arabidopsis thaliana
KW  - biostimulant
KW  - paraquat
KW  - priming
KW  - oxidative stress tolerance
KW  - reactive oxygen species
Y1  - 2019
U6  - https://doi.org/10.3390/ijms21020474
SN  - 1422-0067
VL  - 21
IS  - 2
PB  - Molecular Diversity Preservation International
CY  - Basel
ER  - 
TY  - JOUR
A1  - Christakoudi, Sofa
A1  - Tsilidis, Konstantinos K.
A1  - Muller, David C.
A1  - Freisling, Heinz
A1  - Weiderpass, Elisabete
A1  - Overvad, Kim
A1  - Söderberg, Stefan
A1  - Häggström, Christel
A1  - Pischon, Tobias
A1  - Dahm, Christina C.
A1  - Zhang, Jie
A1  - Tjønneland, Anne
A1  - Schulze, Matthias Bernd
T1  - A Body Shape Index (ABSI) achieves better mortality risk stratification than alternative indices of abdominal obesity: results from a large European cohort
JF  - Scientific Reports
N2  - Abdominal and general adiposity are independently associated with mortality, but there is no consensus on how best to assess abdominal adiposity. We compared the ability of alternative waist indices to complement body mass index (BMI) when assessing all-cause mortality. We used data from 352,985 participants in the European Prospective Investigation into Cancer and Nutrition (EPIC) and Cox proportional hazards models adjusted for other risk factors. During a mean follow-up of 16.1 years, 38,178 participants died. Combining in one model BMI and a strongly correlated waist index altered the association patterns with mortality, to a predominantly negative association for BMI and a stronger positive association for the waist index, while combining BMI with the uncorrelated A Body Shape Index (ABSI) preserved the association patterns. Sex-specific cohort-wide quartiles of waist indices correlated with BMI could not separate high-risk from low-risk individuals within underweight (BMI<18.5 kg/m(2)) or obese (BMI30 kg/m(2)) categories, while the highest quartile of ABSI separated 18-39% of the individuals within each BMI category, which had 22-55% higher risk of death. In conclusion, only a waist index independent of BMI by design, such as ABSI, complements BMI and enables efficient risk stratification, which could facilitate personalisation of screening, treatment and monitoring.
KW  - all-cause mortality
KW  - anthropometric measures
KW  - mass index
KW  - overweight
KW  - cancer
KW  - prediction
KW  - adiposity
KW  - size
Y1  - 2020
VL  - 10
IS  - 1
PB  - Springer Nature
CY  - Berlin
ER  - 
TY  - GEN
A1  - Christakoudi, Sofa
A1  - Tsilidis, Konstantinos K.
A1  - Muller, David C.
A1  - Freisling, Heinz
A1  - Weiderpass, Elisabete
A1  - Overvad, Kim
A1  - Söderberg, Stefan
A1  - Häggström, Christel
A1  - Pischon, Tobias
A1  - Dahm, Christina C.
A1  - Zhang, Jie
A1  - Tjønneland, Anne
A1  - Schulze, Matthias Bernd
T1  - A Body Shape Index (ABSI) achieves better mortality risk stratification than alternative indices of abdominal obesity: results from a large European cohort
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - Abdominal and general adiposity are independently associated with mortality, but there is no consensus on how best to assess abdominal adiposity. We compared the ability of alternative waist indices to complement body mass index (BMI) when assessing all-cause mortality. We used data from 352,985 participants in the European Prospective Investigation into Cancer and Nutrition (EPIC) and Cox proportional hazards models adjusted for other risk factors. During a mean follow-up of 16.1 years, 38,178 participants died. Combining in one model BMI and a strongly correlated waist index altered the association patterns with mortality, to a predominantly negative association for BMI and a stronger positive association for the waist index, while combining BMI with the uncorrelated A Body Shape Index (ABSI) preserved the association patterns. Sex-specific cohort-wide quartiles of waist indices correlated with BMI could not separate high-risk from low-risk individuals within underweight (BMI<18.5 kg/m(2)) or obese (BMI30 kg/m(2)) categories, while the highest quartile of ABSI separated 18-39% of the individuals within each BMI category, which had 22-55% higher risk of death. In conclusion, only a waist index independent of BMI by design, such as ABSI, complements BMI and enables efficient risk stratification, which could facilitate personalisation of screening, treatment and monitoring.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1200 
KW  - all-cause mortality
KW  - anthropometric measures
KW  - mass index
KW  - overweight
KW  - cancer
KW  - prediction
KW  - adiposity
KW  - size
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-525827
SN  - 1866-8372
IS  - 1
ER  - 
TY  - JOUR
A1  - Haueis, Lisa
A1  - Stech, Marlitt
A1  - Kubick, Stefan
T1  - A Cell-free Expression Pipeline for the Generation and Functional Characterization of Nanobodies
JF  - Frontiers in Bioengineering and Biotechnology
N2  - Cell-free systems are well-established platforms for the rapid synthesis, screening, engineering and modification of all kinds of recombinant proteins ranging from membrane proteins to soluble proteins, enzymes and even toxins. Also within the antibody field the cell-free technology has gained considerable attention with respect to the clinical research pipeline including antibody discovery and production. Besides the classical full-length monoclonal antibodies (mAbs), so-called "nanobodies" (Nbs) have come into focus. A Nb is the smallest naturally-derived functional antibody fragment known and represents the variable domain (VHH, similar to 15 kDa) of a camelid heavy-chain-only antibody (HCAb). Based on their nanoscale and their special structure, Nbs display striking advantages concerning their production, but also their characteristics as binders, such as high stability, diversity, improved tissue penetration and reaching of cavity-like epitopes. The classical way to produce Nbs depends on the use of living cells as production host. Though cell-based production is well-established, it is still time-consuming, laborious and hardly amenable for high-throughput applications. Here, we present for the first time to our knowledge the synthesis of functional Nbs in a standardized mammalian cell-free system based on Chinese hamster ovary (CHO) cell lysates. Cell-free reactions were shown to be time-efficient and easy-to-handle allowing for the "on demand" synthesis of Nbs. Taken together, we complement available methods and demonstrate a promising new system for Nb selection and validation.
KW  - cell-free protein synthesis
KW  - In vitro transcription
KW  - translation
KW  - nanobody
KW  - VHH
KW  - camelid
KW  - CHO cell lysate
Y1  - 2022
U6  - https://doi.org/10.3389/fbioe.2022.896763
SN  - 2296-4185
VL  - 10
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Krebs, Simon K.
A1  - Rakotoarinoro, Nathanael
A1  - Stech, Marlitt
A1  - Zemella, Anne
A1  - Kubick, Stefan
T1  - A CHO-based cell-free dual fluorescence reporter system for the straightforward assessment of amber suppression and scFv functionality
JF  - Frontiers in Bioengineering and Biotechnology
N2  - Incorporation of noncanonical amino acids (ncAAs) with bioorthogonal reactive groups by amber suppression allows the generation of synthetic proteins with desired novel properties. Such modified molecules are in high demand for basic research and therapeutic applications such as cancer treatment and in vivo imaging. The positioning of the ncAA-responsive codon within the protein's coding sequence is critical in order to maintain protein function, achieve high yields of ncAA-containing protein, and allow effective conjugation. Cell-free ncAA incorporation is of particular interest due to the open nature of cell-free systems and their concurrent ease of manipulation. In this study, we report a straightforward workflow to inquire ncAA positions in regard to incorporation efficiency and protein functionality in a Chinese hamster ovary (CHO) cell-free system. As a model, the well-established orthogonal translation components Escherichia coli tyrosyl-tRNA synthetase (TyrRS) and tRNATyr(CUA) were used to site-specifically incorporate the ncAA p-azido-l-phenylalanine (AzF) in response to UAG codons. A total of seven ncAA sites within an anti-epidermal growth factor receptor (EGFR) single-chain variable fragment (scFv) N-terminally fused to the red fluorescent protein mRFP1 and C-terminally fused to the green fluorescent protein sfGFP were investigated for ncAA incorporation efficiency and impact on antigen binding. The characterized cell-free dual fluorescence reporter system allows screening for ncAA incorporation sites with high incorporation efficiency that maintain protein activity. It is parallelizable, scalable, and easy to operate. We propose that the established CHO-based cell-free dual fluorescence reporter system can be of particular interest for the development of antibody-drug conjugates (ADCs).
KW  - expanded genetic code
KW  - orthogonal system
KW  - noncanonical amino acid
KW  - unnatural amino acid
KW  - antibody
KW  - cell-free protein synthesis
KW  - mRFP1
KW  - sfGFP
Y1  - 2022
U6  - https://doi.org/10.3389/fbioe.2022.873906
SN  - 2296-4185
VL  - 10
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Çabuk, Uğur
A1  - Ünlü, Ercan Selçuk
T1  - A combined de novo assembly approach increases the quality of prokaryotic draft genomes
JF  - Folia microbiologica : international journal for general, environmental and applied microbiology, and immunology
N2  - Next-generation sequencing methods provide comprehensive data for the analysis of structural and functional analysis of the genome. The draft genomes with low contig number and high N50 value can give insight into the structure of the genome as well as provide information on the annotation of the genome. In this study, we designed a pipeline that can be used to assemble prokaryotic draft genomes with low number of contigs and high N50 value. We aimed to use combination of two de novo assembly tools (SPAdes and IDBA-Hybrid) and evaluate the impact of this approach on the quality metrics of the assemblies. The followed pipeline was tested with the raw sequence data with short reads (< 300) for a total of 10 species from four different genera. To obtain the final draft genomes, we firstly assembled the sequences using SPAdes to find closely related organism using the extracted 16 s rRNA from it. IDBA-Hybrid assembler was used to obtain the second assembly data using the closely related organism genome. SPAdes assembler tool was implemented using the second assembly, produced by IDBA-hybrid as a hint. The results were evaluated using QUAST and BUSCO. The pipeline was successful for the reduction of the contig numbers and increasing the N50 statistical values in the draft genome assemblies while preserving the coverage of the draft genomes.
KW  - De novo assembly
KW  - Prokaryotes
KW  - Bacteria
KW  - NGS
KW  - Short reads
KW  - Draft genome
Y1  - 2022
U6  - https://doi.org/10.1007/s12223-022-00980-7
SN  - 0015-5632
SN  - 1874-9356
VL  - 67
SP  - 801
EP  - 810
PB  - Springer
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Mbebi, Alain J.
A1  - Breitler, Jean-Christophe
A1  - Bordeaux, M'elanie
A1  - Sulpice, Ronan
A1  - McHale, Marcus
A1  - Tong, Hao
A1  - Toniutti, Lucile
A1  - Castillo, Jonny Alonso
A1  - Bertrand, Benoit
A1  - Nikoloski, Zoran
T1  - A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids
JF  - G3: Genes, genomes, genetics
N2  - Genomic prediction has revolutionized crop breeding despite remaining issues of transferability of models to unseen environmental conditions and environments. Usage of endophenotypes rather than genomic markers leads to the possibility of building phenomic prediction models that can account, in part, for this challenge. Here, we compare and contrast genomic prediction and phenomic prediction models for 3 growth-related traits, namely, leaf count, tree height, and trunk diameter, from 2 coffee 3-way hybrid populations exposed to a series of treatment-inducing environmental conditions. The models are based on 7 different statistical methods built with genomic markers and ChlF data used as predictors. This comparative analysis demonstrates that the best-performing phenomic prediction models show higher predictability than the best genomic prediction models for the considered traits and environments in the vast majority of comparisons within 3-way hybrid populations. In addition, we show that phenomic prediction models are transferrable between conditions but to a lower extent between populations and we conclude that chlorophyll a fluorescence data can serve as alternative predictors in statistical models of coffee hybrid performance. Future directions will explore their combination with other endophenotypes to further improve the prediction of growth-related traits for crops.
KW  - genomic prediction
KW  - phenomic prediction
KW  - 3-way coffee hybrids
KW  - chlorophyll a fluorescence
KW  - GenPred
KW  - Shared Data Resource
Y1  - 2022
U6  - https://doi.org/10.1093/g3journal/jkac170
SN  - 2160-1836
VL  - 12
IS  - 9
PB  - Genetics Soc. of America
CY  - Pittsburgh, PA
ER  - 
TY  - JOUR
A1  - Zoccarato, Luca
A1  - Sher, Daniel
A1  - Miki, Takeshi
A1  - Segre, Daniel
A1  - Grossart, Hans-Peter
T1  - A comparative whole-genome approach identifies bacterial traits for marine microbial interactions
JF  - Communications biology
N2  - Luca Zoccarato, Daniel Sher et al. leverage publicly available bacterial genomes from marine and other environments to examine traits underlying microbial interactions.
Their results provide a valuable resource to investigate clusters of functional and linked traits to better understand marine bacteria community assembly and dynamics.  

Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. 

We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10% of genomes), phytohormones (3-8%) and different B vitamins (57-70%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. 

Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics.
Y1  - 2022
U6  - https://doi.org/10.1038/s42003-022-03184-4
SN  - 2399-3642
VL  - 5
IS  - 1
PB  - Springer Nature
CY  - Berlin
ER  - 
TY  - JOUR
A1  - Noonan, Michael J.
A1  - Tucker, Marlee A.
A1  - Fleming, Christen H.
A1  - Akre, Thomas S.
A1  - Alberts, Susan C.
A1  - Ali, Abdullahi H.
A1  - Altmann, Jeanne
A1  - Antunes, Pamela Castro
A1  - Belant, Jerrold L.
A1  - Beyer, Dean
A1  - Blaum, Niels
A1  - Boehning-Gaese, Katrin
A1  - Cullen Jr, Laury
A1  - de Paula, Rogerio Cunha
A1  - Dekker, Jasja
A1  - Drescher-Lehman, Jonathan
A1  - Farwig, Nina
A1  - Fichtel, Claudia
A1  - Fischer, Christina
A1  - Ford, Adam T.
A1  - Goheen, Jacob R.
A1  - Janssen, Rene
A1  - Jeltsch, Florian
A1  - Kauffman, Matthew
A1  - Kappeler, Peter M.
A1  - Koch, Flavia
A1  - LaPoint, Scott
A1  - Markham, A. Catherine
A1  - Medici, Emilia Patricia
A1  - Morato, Ronaldo G.
A1  - Nathan, Ran
A1  - Oliveira-Santos, Luiz Gustavo R.
A1  - Olson, Kirk A.
A1  - Patterson, Bruce D.
A1  - Paviolo, Agustin
A1  - Ramalho, Emiliano Estero
A1  - Rosner, Sascha
A1  - Schabo, Dana G.
A1  - Selva, Nuria
A1  - Sergiel, Agnieszka
A1  - da Silva, Marina Xavier
A1  - Spiegel, Orr
A1  - Thompson, Peter
A1  - Ullmann, Wiebke
A1  - Zieba, Filip
A1  - Zwijacz-Kozica, Tomasz
A1  - Fagan, William F.
A1  - Mueller, Thomas
A1  - Calabrese, Justin M.
T1  - A comprehensive analysis of autocorrelation and bias in home range estimation
JF  - Ecological monographs : a publication of the Ecological Society of America.
N2  - Home range estimation is routine practice in ecological research. While advances in animal tracking technology have increased our capacity to collect data to support home range analysis, these same advances have also resulted in increasingly autocorrelated data. Consequently, the question of which home range estimator to use on modern, highly autocorrelated tracking data remains open. This question is particularly relevant given that most estimators assume independently sampled data. Here, we provide a comprehensive evaluation of the effects of autocorrelation on home range estimation. We base our study on an extensive data set of GPS locations from 369 individuals representing 27 species distributed across five continents. We first assemble a broad array of home range estimators, including Kernel Density Estimation (KDE) with four bandwidth optimizers (Gaussian reference function, autocorrelated‐Gaussian reference function [AKDE], Silverman's rule of thumb, and least squares cross‐validation), Minimum Convex Polygon, and Local Convex Hull methods. Notably, all of these estimators except AKDE assume independent and identically distributed (IID) data. We then employ half‐sample cross‐validation to objectively quantify estimator performance, and the recently introduced effective sample size for home range area estimation ( N̂ area
) to quantify the information content of each data set. We found that AKDE 95% area estimates were larger than conventional IID‐based estimates by a mean factor of 2. The median number of cross‐validated locations included in the hold‐out sets by AKDE 95% (or 50%) estimates was 95.3% (or 50.1%), confirming the larger AKDE ranges were appropriately selective at the specified quantile. Conversely, conventional estimates exhibited negative bias that increased with decreasing N̂ area. To contextualize our empirical results, we performed a detailed simulation study to tease apart how sampling frequency, sampling duration, and the focal animal's movement conspire to affect range estimates. Paralleling our empirical results, the simulation study demonstrated that AKDE was generally more accurate than conventional methods, particularly for small N̂ area. While 72% of the 369 empirical data sets had >1,000 total observations, only 4% had an N̂ area >1,000, where 30% had an N̂ area <30. In this frequently encountered scenario of small N̂ area, AKDE was the only estimator capable of producing an accurate home range estimate on autocorrelated data.
KW  - animal movement
KW  - kernel density estimation
KW  - local convex hull
KW  - minimum convex polygon
KW  - range distribution
KW  - space use
KW  - telemetry
KW  - tracking data
Y1  - 2018
U6  - https://doi.org/10.1002/ecm.1344
SN  - 0012-9615
SN  - 1557-7015
VL  - 89
IS  - 2
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Palkopoulou, Eleftheria
A1  - Lipson, Mark
A1  - Mallick, Swapan
A1  - Nielsen, Svend
A1  - Rohland, Nadin
A1  - Baleka, Sina Isabelle
A1  - Karpinski, Emil
A1  - Ivancevici, Atma M.
A1  - Thu-Hien To, 
A1  - Kortschak, Daniel
A1  - Raison, Joy M.
A1  - Qu, Zhipeng
A1  - Chin, Tat-Jun
A1  - Alt, Kurt W.
A1  - Claesson, Stefan
A1  - Dalen, Love
A1  - MacPhee, Ross D. E.
A1  - Meller, Harald
A1  - Rocar, Alfred L.
A1  - Ryder, Oliver A.
A1  - Heiman, David
A1  - Young, Sarah
A1  - Breen, Matthew
A1  - Williams, Christina
A1  - Aken, Bronwen L.
A1  - Ruffier, Magali
A1  - Karlsson, Elinor
A1  - Johnson, Jeremy
A1  - Di Palma, Federica
A1  - Alfoldi, Jessica
A1  - Adelsoni, David L.
A1  - Mailund, Thomas
A1  - Munch, Kasper
A1  - Lindblad-Toh, Kerstin
A1  - Hofreiter, Michael
A1  - Poinar, Hendrik
A1  - Reich, David
T1  - A comprehensive genomic history of extinct and living elephants
JF  - Proceedings of the National Academy of Sciences of the United States of America
KW  - paleogenomics
KW  - elephantid evolution
KW  - mammoth
KW  - admixture
KW  - species divergence
Y1  - 2018
U6  - https://doi.org/10.1073/pnas.1720554115
SN  - 0027-8424
VL  - 115
IS  - 11
SP  - E2566
EP  - E2574
PB  - National Acad. of Sciences
CY  - Washington
ER  - 
TY  - JOUR
A1  - Chapman, Eric M.
A1  - Lant, Benjamin
A1  - Ohashi, Yota
A1  - Yu, Bin
A1  - Schertzberg, Michael
A1  - Go, Christopher
A1  - Dogra, Deepika
A1  - Koskimaki, Janne
A1  - Girard, Romuald
A1  - Li, Yan
A1  - Fraser, Andrew G.
A1  - Awad, Issam A.
A1  - Abdelilah-Seyfried, Salim
A1  - Gingras, Anne-Claude
A1  - Derry, William Brent
T1  - A conserved CCM complex promotes apoptosis non-autonomously by regulating zinc homeostasis
JF  - Nature Communications
N2  - Apoptotic death of cells damaged by genotoxic stress requires regulatory input from surrounding tissues. The C. elegans scaffold protein KRI-1, ortholog of mammalian KRIT1/CCM1, permits DNA damage-induced apoptosis of cells in the germline by an unknown cell non-autonomous mechanism. We reveal that KRI-1 exists in a complex with CCM-2 in the intestine to negatively regulate the ERK-5/MAPK pathway. This allows the KLF-3 transcription factor to facilitate expression of the SLC39 zinc transporter gene zipt-2.3, which functions to sequester zinc in the intestine. Ablation of KRI-1 results in reduced zinc sequestration in the intestine, inhibition of IR-induced MPK-1/ERK1 activation, and apoptosis in the germline. Zinc localization is also perturbed in the vasculature of krit1(-/-) zebrafish, and SLC39 zinc transporters are mis-expressed in Cerebral Cavernous Malformations (CCM) patient tissues. This study provides new insights into the regulation of apoptosis by cross-tissue communication, and suggests a link between zinc localization and CCM disease.
Y1  - 2019
U6  - https://doi.org/10.1038/s41467-019-09829-z
SN  - 2041-1723
VL  - 10
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - GEN
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
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1161 
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  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-522081
SN  - 1866-8372
IS  - 9
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  - Buyinza, Daniel
A1  - Derese, Solomon
A1  - Ndakala, Albert
A1  - Heydenreich, Matthias
A1  - Yenesew, Abiy
A1  - Koch, Andreas
A1  - Oriko, Richard
T1  - A coumestan and a coumaronochromone from Millettia lasiantha
JF  - Biochemical systematics and ecology
N2  - The manuscript describes the phytochemical investigation of the roots, leaves and stem bark of Millettia lasiantha resulting in the isolation of twelve compounds including two new isomeric isoflavones lascoumestan and las-coumaronochromone. The structures of the new compounds were determined using different spectroscopic techniques.
KW  - Millettia lasiantha
KW  - Leguminosae
KW  - Coumestan
KW  - Coumaronochromone
Y1  - 2021
U6  - https://doi.org/10.1016/j.bse.2021.104277
SN  - 0305-1978
SN  - 1873-2925
VL  - 97
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Luetkecosmann, Steffi
A1  - Faupel, Thomas
A1  - Porstmann, Silvia
A1  - Porstmann, Tomas
A1  - Micheel, Burkhard
A1  - Hanack, Katja
T1  - A cross-reactive monoclonal antibody as universal detection antibody in autoantibody diagnostic assays
JF  - Clinica chimica acta
N2  - Diagnostics of Autoimmune Diseases involve screening of patient samples for containing autoantibodies against various antigens. To ensure quality of diagnostic assays a calibrator is needed in each assay system. Different calibrators as recombinant human monoclonal antibodies as well as chimeric antibodies against the autoantigens of interest are described. A less cost-intensive and also more representative possibility covering different targets on the antigens is the utilization of polyclonal sera from other species. Nevertheless, the detection of human autoantibodies as well as the calibration reagent containing antibodies from other species in one assay constitutes a challenge in terms of assay calibration. We therefore developed a cross-reactive monoclonal antibody which binds human as well as rabbit sera with similar affinities in the nanomolar range. We tested our monoclonal antibody S38CD11B12 successfully in the commercial Serazym (R) Anti-Cardiolipin-beta 2-GPI IgG/IgM assay and could thereby prove the eligibility of S38CD11B12 as detection antibody in autoimmune diagnostic assays using rabbit derived sera as reference material.
KW  - Monoclonal antibody
KW  - Detection
KW  - Autoimmune diagnostics
KW  - Cross reactivity
KW  - Assay calibration
Y1  - 2019
U6  - https://doi.org/10.1016/j.cca.2019.09.003
SN  - 0009-8981
SN  - 1873-3492
VL  - 499
SP  - 87
EP  - 92
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Demal, Till Joscha
A1  - Heise, Melina
A1  - Reiz, Benedikt
A1  - Dogra, Deepika
A1  - Braenne, Ingrid
A1  - Reichenspurner, Hermann
A1  - Männer, Jörg
A1  - Aherrahrou, Zouhair
A1  - Schunkert, Heribert
A1  - Erdmann, Jeanette
A1  - Abdelilah-Seyfried, Salim
T1  - A familial congenital heart disease with a possible multigenic origin involving a mutation in BMPR1A
JF  - Scientific reports
N2  - The genetics of many congenital heart diseases (CHDs) can only unsatisfactorily be explained by known chromosomal or Mendelian syndromes. Here, we present sequencing data of a family with a potentially multigenic origin of CHD. Twelve of nineteen family members carry a familial mutation [NM_004329.2:c.1328 G > A (p.R443H)] which encodes a predicted deleterious variant of BMPR1A. This mutation co-segregates with a linkage region on chromosome 1 that associates with the emergence of severe CHDs including Ebstein’s anomaly, atrioventricular septal defect, and others. We show that the continuous overexpression of the zebrafish homologous mutation bmpr1aap.R438H within endocardium causes a reduced AV valve area, a downregulation of Wnt/ß-catenin signalling at the AV canal, and growth of additional tissue mass in adult zebrafish hearts. This finding opens the possibility of testing genetic interactions between BMPR1A and other candidate genes within linkage region 1 which may provide a first step towards unravelling more complex genetic patterns in cardiovascular disease aetiology.
Y1  - 2019
U6  - https://doi.org/10.1038/s41598-019-39648-7
SN  - 2045-2322
VL  - 9
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Xiao, Shangbin
A1  - Liu, Liu
A1  - Wang, Wei
A1  - Lorke, Andreas
A1  - Woodhouse, Jason Nicholas
A1  - Grossart, Hans-Peter
T1  - A Fast-Response Automated Gas Equilibrator (FaRAGE) for continuous in situ measurement of CH4 and CO2 dissolved in water
JF  - Hydrology and earth system sciences : HESS
N2  - Biogenic greenhouse gas emissions, e.g., of methane (CH4) and carbon dioxide (CO2) from inland waters, contribute substantially to global warming. In aquatic systems, dissolved greenhouse gases are highly heterogeneous in both space and time. To better understand the biological and physical processes that affect sources and sinks of both CH4 and CO2, their dissolved concentrations need to be measured with high spatial and temporal resolution. To achieve this goal, we developed the Fast-Response Automated Gas Equilibrator (FaRAGE) for real-time in situ measurement of dissolved CH4 and CO2 concentrations at the water surface and in the water column. FaRAGE can achieve an exceptionally short response time (t(95%) = 12 s when including the response time of the gas analyzer) while retaining an equilibration ratio of 62.6% and a measurement accuracy of 0.5% for CH4. A similar performance was observed for dissolved CO2 (t(95%) = 10 s, equilibration ratio 67.1 %). An equilibration ratio as high as 91.8% can be reached at the cost of a slightly increased response time (16 s). The FaRAGE is capable of continuously measuring dissolved CO2 and CH4 concentrations in the nM-to-submM (10(-9)-10(-3) mol L-1) range with a detection limit of subnM (10(-10) mol L-1), when coupling with a cavity ring-down greenhouse gas analyzer (Picarro GasScouter). FaRAGE allows for the possibility of mapping dissolved concentration in a "quasi" three-dimensional manner in lakes and provides an inexpensive alternative to other commercial gas equilibrators. It is simple to operate and suitable for continuous monitoring with a strong tolerance for suspended particles. While the FaRAGE is developed for inland waters, it can be also applied to ocean waters by tuning the gas-water mixing ratio. The FaRAGE is easily adapted to suit other gas analyzers expanding the range of potential applications, including nitrous oxide and isotopic composition of the gases.
Y1  - 2020
U6  - https://doi.org/10.5194/hess-24-3871-2020
SN  - 1027-5606
SN  - 1607-7938
VL  - 24
IS  - 7
SP  - 3871
EP  - 3880
PB  - European Geosciences Union (EGU) ; Copernicus
CY  - Munich
ER  - 
TY  - GEN
A1  - Roethlein, Christoph
A1  - Miettinen, Markus S.
A1  - Ignatova, Zoya
T1  - A flexible approach to assess fluorescence decay functions in complex energy transfer systems
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe 819
N2  - Background: Time-correlated Forster resonance energy transfer (FRET) probes molecular distances with greater accuracy than intensity-based calculation of FRET efficiency and provides a powerful tool to study biomolecular structure and dynamics. Moreover, time-correlated photon count measurements bear additional information on the variety of donor surroundings allowing more detailed differentiation between distinct structural geometries which are typically inaccessible to general fitting solutions.

Results: Here we develop a new approach based on Monte Carlo simulations of time-correlated FRET events to estimate the time-correlated single photon counts (TCSPC) histograms in complex systems. This simulation solution assesses the full statistics of time-correlated photon counts and distance distributions of fluorescently labeled biomolecules. The simulations are consistent with the theoretical predictions of the dye behavior in FRET systems with defined dye distances and measurements of randomly distributed dye solutions. We validate the simulation results using a highly heterogeneous aggregation system and explore the conditions to use this tool in complex systems.

Conclusion: This approach is powerful in distinguishing distance distributions in a wide variety of experimental setups, thus providing a versatile tool to accurately distinguish between different structural assemblies in highly complex systems.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 819 
KW  - time resolved FRET
KW  - Monte-Carlo simulations
KW  - complex heterogeneous systems
KW  - protein aggregation
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-427557
SN  - 1866-8372
IS  - 819
ER  - 
TY  - JOUR
A1  - Sharma, Neha
A1  - Ruelens, Philip
A1  - Maggen, Thomas
A1  - Dochy, Niklas
A1  - Torfs, Sanne
A1  - Kaufmann, Kerstin
A1  - Rohde, Antje
A1  - Geuten, Koen
T1  - A Flowering Locus C Homolog Is a Vernalization-Regulated Repressor in Brachypodium and Is Cold Regulated in Wheat
JF  - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants
N2  - Winter cereals require prolonged cold to transition from vegetative to reproductive development. This process, referred to as vernalization, has been extensively studied in Arabidopsis (Arabidopsis thaliana). In Arabidopsis, a key flowering repressor called FLOWERING LOCUS C (FLC) quantitatively controls the vernalization requirement. By contrast, in cereals, the vernalization response is mainly regulated by the VERNALIZATION genes, VRN1 and VRN2. Here, we characterize ODDSOC2, a recently identified FLC ortholog in monocots, knowing that it belongs to the FLC lineage. By studying its expression in a diverse set of Brachypodium accessions, we find that it is a good predictor of the vernalization requirement. Analyses of transgenics demonstrated that BdODDSOC2 functions as a vernalization-regulated flowering repressor. In most Brachypodium accessions BdODDSOC2 is down-regulated by cold, and in one of the winter accessions in which this down-regulation was evident, BdODDSOC2 responded to cold before BdVRN1. When stably down-regulated, the mechanism is associated with spreading H3K27me3 modifications at the BdODDSOC2 chromatin. Finally, homoeolog-specific gene expression analyses identify TaAGL33 and its splice variant TaAGL22 as the FLC orthologs in wheat (Triticum aestivum) behaving most similar to Brachypodium ODDSOC2. Overall, our study suggests that ODDSOC2 is not only phylogenetically related to FLC in eudicots but also functions as a flowering repressor in the vernalization pathway of Brachypodium and likely other temperate grasses. These insights could prove useful in breeding efforts to refine the vernalization requirement of temperate cereals and adapt varieties to changing climates.
Y1  - 2016
U6  - https://doi.org/10.1104/pp.16.01161
SN  - 0032-0889
SN  - 1532-2548
VL  - 173
IS  - 2
SP  - 1301
EP  - 1315
PB  - American Society of Plant Physiologists
CY  - Rockville
ER  - 
TY  - GEN
A1  - Liaimer, Anton
A1  - Jensen, John B.
A1  - Dittmann-Thünemann, Elke
T1  - A genetic and chemical perspective on symbiotic recruitment of cyanobacteria of the genus Nostoc into the host plant Blasia pusilla L.
T2  - Frontiers in microbiology
N2  - Liverwort Blasia pusilla L. recruits soil nitrogen-fixing cyanobacteria of genus Nostoc as symbiotic partners. In this work we compared Nostoc community composition inside the plants and in the soil around them from two distant locations in Northern Norway. STRR fingerprinting and 16S rDNA phylogeny reconstruction showed a remarkable local diversity among isolates assigned to several Nostoc clades. An extensive web of negative allelopathic interactions was recorded at an agricultural site, but not at the undisturbed natural site. The cell extracts of the cyanobacteria did not show antimicrobial activities, but four isolates were shown to be cytotoxic to human cells. The secondary metabolite profiles of the isolates were mapped by MALDI-TOF MS, and the most prominent ions were further analyzed by Q-TOF for MS/MS aided identification. Symbiotic isolates produced a great variety of small peptide-like substances, most of which lack any record in the databases. Among identified compounds we found microcystin and nodularin variants toxic to eukaryotic cells. Microcystin producing chemotypes were dominating as symbiotic recruits but not in the free-living community. In addition, we were able to identify several novel aeruginosins and banyaside-like compounds, as well as nostocyclopeptides and nosperin.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 434 
KW  - cyanobacteria
KW  - secondary metabolites
KW  - symbiosis
KW  - Blasia
KW  - Nostoc
KW  - allelopathy
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407179
ER  - 
TY  - JOUR
A1  - Lah, Ljerka
A1  - Löber, Ulrike
A1  - Hsiang, Tom
A1  - Hartmann, Stefanie
T1  - A genomic comparison of putative pathogenicity-related gene families in five members of the Ophiostomatales with different lifestyles
JF  - Fungal biology
N2  - Ophiostomatoid fungi are vectored by their bark-beetle associates and colonize different host tree species. To survive and proliferate in the host, they have evolved mechanisms for detoxification and elimination of host defence compounds, efficient nutrient sequestration, and, in pathogenic species, virulence towards plants. Here, we assembled a draft genome of the spruce pathogen Ophiostoma bicolor. For our comparative and phylogenetic analyses, we mined the genomes of closely related species (Ophiostoma piceae, Ophiostoma ulmi, Ophiostoma novo-ulmi, and Grosmannia clavigera). Our aim was to acquire a genomic and evolutionary perspective of gene families important in host colonization. Genome comparisons showed that both the nuclear and mitochondrial genomes in our assembly were largely complete. Our O. bicolor 25.3 Mbp draft genome had 10 018 predicted genes, 6041 proteins with gene ontology (GO) annotation, 269 carbohydrate-active enzymes (CAZymes), 559 peptidases and inhibitors, and 1373 genes likely involved in pathogen-host interactions. Phylogenetic analyses of selected protein families revealed core sets of cytochrome P450 genes, ABC transporters and backbone genes involved in secondary metabolite (SM) biosynthesis (polyketide synthases (PKS) and non-ribosomal synthases), and species-specific gene losses and duplications. Phylogenetic analyses of protein families of interest provided insight into evolutionary adaptations to host biochemistry in ophiostomatoid fungi.
KW  - Bark beetle
KW  - Bluestain fungi
KW  - Ips typographus
Y1  - 2016
U6  - https://doi.org/10.1016/j.funbio.2016.12.002
SN  - 1878-6146
SN  - 1878-6162
VL  - 121
SP  - 234
EP  - 252
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - GEN
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
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1189 
KW  - transient expression
KW  - agro-infiltration
KW  - subcellular localization
KW  - protein-protein interaction
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-524254
SN  - 1866-8372
IS  - 5
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  - GEN
A1  - Dortay, Hakan
A1  - Müller-Röber, Bernd
T1  - A highly efficient pipeline for protein expression in Leishmania tarentolae sing infrared fluorescence protein as marker
N2  - Background: Leishmania tarentolae, a unicellular eukaryotic protozoan, has been established as a novel host for recombinant protein production in recent years. Current protocols for protein expression in Leishmania are, however, time consuming and require extensive lab work in order to identify well-expressing cell lines. Here we established an alternative protein expression work-flow that employs recently engineered infrared fluorescence protein (IFP) as a suitable and easy-to-handle reporter protein for recombinant protein expression in Leishmania. As model proteins we tested three proteins from the plant Arabidopsis thaliana, including a NAC and a type-B ARR transcription factor. Results: IFP and IFP fusion proteins were expressed in Leishmania and rapidly detected in cells by deconvolution microscopy and in culture by infrared imaging of 96-well microtiter plates using small cell culture volumes (2 μL - 100 μL). Motility, shape and growth of Leishmania cells were not impaired by intracellular accumulation of IFP. In-cell detection of IFP and IFP fusion proteins was straightforward already at the beginning of the expression pipeline and thus allowed early pre-selection of well-expressing Leishmania clones. Furthermore, IFP fusion proteins retained infrared fluorescence after electrophoresis in denaturing SDS-polyacrylamide gels, allowing direct in-gel detection without the need to disassemble cast protein gels. Thus, parameters for scaling up protein production and streamlining purification routes can be easily optimized when employing IFP as reporter. Conclusions: Using IFP as biosensor we devised a protocol for rapid and convenient protein expression in Leishmania tarentolae. Our expression pipeline is superior to previously established methods in that it significantly reduces the hands-on-time and work load required for identifying well-expressing clones, refining protein production parameters and establishing purification protocols. The facile in-cell and in-gel detection tools built on IFP make Leishmania amenable for high-throughput expression of proteins from plant and animal sources.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 122 
KW  - System
KW  - Donovani
Y1  - 2010
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44773
ER  - 
TY  - GEN
A1  - Dortay, Hakan
A1  - Müller-Röber, Bernd
T1  - A highly efficient pipeline for protein expression in Leishmania tarentolae using infrared fluorescence protein as marker
N2  - Background: Leishmania tarentolae, a unicellular eukaryotic protozoan, has been established as a novel host for recombinant protein production in recent years. Current protocols for protein expression in Leishmania are, however, time consuming and require extensive lab work in order to identify well-expressing cell lines. Here we established an alternative protein expression work-flow that employs recently engineered infrared fluorescence protein (IFP) as a suitable and easy-to-handle reporter protein for recombinant protein expression in Leishmania. As model proteins we tested three proteins from the plant Arabidopsis thaliana, including a NAC and a type-B ARR transcription factor.

Results: IFP and IFP fusion proteins were expressed in Leishmania and rapidly detected in cells by deconvolution microscopy and in culture by infrared imaging of 96-well microtiter plates using small cell culture volumes (2 mu L - 100 mu L). Motility, shape and growth of Leishmania cells were not impaired by intracellular accumulation of IFP. In-cell detection of IFP and IFP fusion proteins was straightforward already at the beginning of the expression pipeline and thus allowed early pre-selection of well-expressing Leishmania clones. Furthermore, IFP fusion proteins retained infrared fluorescence after electrophoresis in denaturing SDS-polyacrylamide gels, allowing direct in-gel detection without the need to disassemble cast protein gels. Thus, parameters for scaling up protein production and streamlining purification routes can be easily optimized when employing IFP as reporter.

Conclusions: Using IFP as biosensor we devised a protocol for rapid and convenient protein expression in Leishmania tarentolae. Our expression pipeline is superior to previously established methods in that it significantly reduces the hands-on-time and work load required for identifying well-expressing clones, refining protein production parameters and establishing purification protocols. The facile in-cell and in-gel detection tools built on IFP make Leishmania amenable for high-throughput expression of proteins from plant and animal sources.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 366 
KW  - System
KW  - Donovani
Y1  - 2017
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400876
ER  - 
TY  - GEN
A1  - Jantzen, Friederike
A1  - Wozniak, Natalia Joanna
A1  - Kappel, Christian
A1  - Sicard, Adrien
A1  - Lenhard, Michael
T1  - A high‑throughput amplicon‑based method for estimating outcrossing rates
T2  - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe
N2  - Background: The outcrossing rate is a key determinant of the population-genetic structure of species and their long-term evolutionary trajectories. However, determining the outcrossing rate using current methods based on PCRgenotyping individual offspring of focal plants for multiple polymorphic markers is laborious and time-consuming.

Results: We have developed an amplicon-based, high-throughput enabled method for estimating the outcrossing rate and have applied this to an example of scented versus non-scented Capsella (Shepherd’s Purse) genotypes. Our results show that the method is able to robustly capture differences in outcrossing rates. They also highlight potential biases in the estimates resulting from differential haplotype sharing of the focal plants with the pollen-donor population at individual amplicons.

Conclusions: This novel method for estimating outcrossing rates will allow determining this key population-genetic parameter with high-throughput across many genotypes in a population, enabling studies into the genetic determinants of successful pollinator attraction and outcrossing.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 745 
KW  - Outcrossing
KW  - Mixed mating
KW  - Outcrossing rate
KW  - Capsella
KW  - Amplicon sequencing
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-435657
SN  - 1866-8372
IS  - 745
ER  - 
TY  - JOUR
A1  - Jantzen, Friederike
A1  - Wozniak, Natalia Joanna
A1  - Kappel, Christian
A1  - Sicard, Adrien
A1  - Lenhard, Michael
T1  - A high‑throughput amplicon‑based method for estimating outcrossing rates
JF  - Plant Methods
N2  - Background: The outcrossing rate is a key determinant of the population-genetic structure of species and their long-term evolutionary trajectories. However, determining the outcrossing rate using current methods based on PCRgenotyping individual offspring of focal plants for multiple polymorphic markers is laborious and time-consuming.

Results: We have developed an amplicon-based, high-throughput enabled method for estimating the outcrossing rate and have applied this to an example of scented versus non-scented Capsella (Shepherd’s Purse) genotypes. Our results show that the method is able to robustly capture differences in outcrossing rates. They also highlight potential biases in the estimates resulting from differential haplotype sharing of the focal plants with the pollen-donor population at individual amplicons.

Conclusions: This novel method for estimating outcrossing rates will allow determining this key population-genetic parameter with high-throughput across many genotypes in a population, enabling studies into the genetic determinants of successful pollinator attraction and outcrossing.
KW  - Outcrossing
KW  - Mixed mating
KW  - Outcrossing rate
KW  - Capsella
KW  - Amplicon sequencing
Y1  - 2019
U6  - https://doi.org/10.1186/s13007-019-0433-9
SN  - 1746-4811
VL  - 15
IS  - 47
PB  - BioMed Central
CY  - London
ER  - 
TY  - GEN
A1  - Cox, Tom
A1  - Maris, Tom
A1  - Soetart, Karline
A1  - Conley, Daniel
A1  - van Damme, Stefan
A1  - Meire, Patrick
A1  - Middelburg, Jack J.
A1  - Vos, Matthijs
A1  - Struyf, Eric
T1  - A macro-tidal freshwater ecosystem recovering from hypereutrophication : the Schelde lease study
N2  - We report a 40 year record of eutrophication and hypoxia on an estuarine ecosystem and its recovery from hypereutrophication. After decades of high inorganic nutrient concentrations and recurring anoxia and hypoxia, we observe a paradoxical increase in chlorophyll-a concentrations with decreasing nutrient inputs. We hypothesise that algal growth was inhibited due to hypereutrophication, either by elevated ammonium concentrations, severe hypoxia or the production of harmful substances in such a reduced environment. We study the dynamics of a simple but realistic mathematical model, incorporating the assumption of algal growth inhibition. It shows a high algal biomass, net oxygen production equilibrium with low ammonia inputs, and a low algal biomass, net oxygen consumption equilibrium with high ammonia inputs. At intermediate ammonia inputs it displays two alternative stable states. Although not intentional, the numerical output of this model corresponds to observations, giving extra support for assumption of algal growth inhibition. Due to potential algal growth inhibition, the recovery of hypereutrophied systems towards a classical eutrophied state, will need reduction of waste loads below certain thresholds and will be accompanied by large fluctuations in oxygen concentrations. We conclude that also flow-through systems, heavily influenced by external forcings which partly mask internal system dynamics, can display multiple stable states.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 144 
KW  - Estuary SW Netherlands
KW  - southern North-Sea
KW  - Past 50 years
KW  - Westerschelde estuary
KW  - Marine ecosystems
Y1  - 2009
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45180
ER  - 
TY  - JOUR
A1  - Wandt, Viktoria Klara Veronika
A1  - Winkelbeiner, Nicola Lisa
A1  - Bornhorst, Julia
A1  - Witt, Barbara
A1  - Raschke, Stefanie
A1  - Simon, Luise
A1  - Ebert, Franziska
A1  - Kipp, Anna Patricia
A1  - Schwerdtle, Tanja
T1  - A matter of concern
BT  - trace element dyshomeostasis and genomic stability in neurons
JF  - Redox Biology
N2  - Neurons are post-mitotic cells in the brain and their integrity is of central importance to avoid neurodegeneration. Yet, the inability of self-replenishment of post-mitotic cells results in the need to withstand challenges from numerous stressors during life. Neurons are exposed to oxidative stress due to high oxygen consumption during metabolic activity in the brain. Accordingly, DNA damage can occur and accumulate, resulting in genome instability. In this context, imbalances in brain trace element homeostasis are a matter of concern, especially regarding iron, copper, manganese, zinc, and selenium. Although trace elements are essential for brain physiology, excess and deficient conditions are considered to impair neuronal maintenance. Besides increasing oxidative stress, DNA damage response and repair of oxidative DNA damage are affected by trace elements. Hence, a balanced trace element homeostasis is of particular importance to safeguard neuronal genome integrity and prevent neuronal loss. This review summarises the current state of knowledge on the impact of deficient, as well as excessive iron, copper, manganese, zinc, and selenium levels on neuronal genome stability
Y1  - 2021
U6  - https://doi.org/10.1016/j.redox.2021.101877
VL  - 41
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Hartung, Niklas
A1  - Borghardt, Jens Markus
T1  - A mechanistic framework for a priori pharmacokinetic predictions of orally inhaled drugs
JF  - PLoS Computational Biology : a new community journal
N2  - Author summary <br /> The use of orally inhaled drugs for treating lung diseases is appealing since they have the potential for lung selectivity, i.e. high exposure at the site of action -the lung- without excessive side effects. However, the degree of lung selectivity depends on a large number of factors, including physiochemical properties of drug molecules, patient disease state, and inhalation devices. To predict the impact of these factors on drug exposure and thereby to understand the characteristics of an optimal drug for inhalation, we develop a predictive mathematical framework (a "pharmacokinetic model"). In contrast to previous approaches, our model allows combining knowledge from different sources appropriately and its predictions were able to adequately predict different sets of clinical data. Finally, we compare the impact of different factors and find that the most important factors are the size of the inhaled particles, the affinity of the drug to the lung tissue, as well as the rate of drug dissolution in the lung. In contrast to the common belief, the solubility of a drug in the lining fluids is not found to be relevant. These findings are important to understand how inhaled drugs should be designed to achieve best treatment results in patients. <br /> The fate of orally inhaled drugs is determined by pulmonary pharmacokinetic processes such as particle deposition, pulmonary drug dissolution, and mucociliary clearance. Even though each single process has been systematically investigated, a quantitative understanding on the interaction of processes remains limited and therefore identifying optimal drug and formulation characteristics for orally inhaled drugs is still challenging. To investigate this complex interplay, the pulmonary processes can be integrated into mathematical models. However, existing modeling attempts considerably simplify these processes or are not systematically evaluated against (clinical) data. In this work, we developed a mathematical framework based on physiologically-structured population equations to integrate all relevant pulmonary processes mechanistically. A tailored numerical resolution strategy was chosen and the mechanistic model was evaluated systematically against data from different clinical studies. Without adapting the mechanistic model or estimating kinetic parameters based on individual study data, the developed model was able to predict simultaneously (i) lung retention profiles of inhaled insoluble particles, (ii) particle size-dependent pharmacokinetics of inhaled monodisperse particles, (iii) pharmacokinetic differences between inhaled fluticasone propionate and budesonide, as well as (iv) pharmacokinetic differences between healthy volunteers and asthmatic patients. Finally, to identify the most impactful optimization criteria for orally inhaled drugs, the developed mechanistic model was applied to investigate the impact of input parameters on both the pulmonary and systemic exposure. Interestingly, the solubility of the inhaled drug did not have any relevant impact on the local and systemic pharmacokinetics. Instead, the pulmonary dissolution rate, the particle size, the tissue affinity, and the systemic clearance were the most impactful potential optimization parameters. In the future, the developed prediction framework should be considered a powerful tool for identifying optimal drug and formulation characteristics.
Y1  - 2020
U6  - https://doi.org/10.1371/journal.pcbi.1008466
SN  - 1553-734X
SN  - 1553-7358
VL  - 16
IS  - 12
PB  - PLoS
CY  - San Fransisco
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  - THES
A1  - Kirschbaum, Michael
T1  - A microfluidic approach for the initiation and investigation of surface-mediated signal transduction processes on a single-cell level
T1  - Entwicklung einer mikrofluidischen Prozesslinie für die Induktion und Analyse oberflächenvermittelter Signaltransduktionsprozesse auf Einzelzell-Ebene
N2  - For the elucidation of the dynamics of signal transduction processes that are induced by cellular interactions, defined events along the signal transduction cascade and subsequent activation steps have to be analyzed and then also correlated with each other. This cannot be achieved by ensemble measurements because averaging biological data ignores the variability in timing and response patterns of individual cells and leads to highly blurred results. Instead, only a multi-parameter analysis at a single-cell level is able to exploit the information that is crucially needed for deducing the signaling pathways involved. The aim of this work was to develop a process line that allows the initiation of cell-cell or cell-particle interactions while at the same time the induced cellular reactions can be analyzed at various stages along the signal transduction cascade and correlated with each other. As this approach requires the gentle management of individually addressable cells, a dielectrophoresis (DEP)-based microfluidic system was employed that provides the manipulation of microscale objects with very high spatiotemporal precision and without the need of contacting the cell membrane. The system offers a high potential for automation and parallelization. This is essential for achieving a high level of robustness and reproducibility, which are key requirements in order to qualify this approach for a biomedical application. As an example process for intercellular communication, T cell activation has been chosen. The activation of the single T cells was triggered by contacting them individually with microbeads that were coated with antibodies directed against specific cell surface proteins, like the T cell receptor-associated kinase CD3 and the costimulatory molecule CD28 (CD; cluster of differentiation). The stimulation of the cells with the functionalized beads led to a rapid rise of their cytosolic Ca2+ concentration which was analyzed by a dual-wavelength ratiometric fluorescence measurement of the Ca2+-sensitive dye Fura-2. After Ca2+ imaging, the cells were isolated individually from the microfluidic system and cultivated further. Cell division and expression of the marker molecule CD69 as a late activation event of great significance were analyzed the following day and correlated with the previously recorded Ca2+ traces for each individual cell. It turned out such that the temporal profile of the Ca2+ traces between both activated and non-activated cells as well as dividing and non-dividing cells differed significantly. This shows that the pattern of Ca2+ signals in T cells can provide early information about a later reaction of the cell. As isolated cells are highly delicate objects, a precondition for these experiments was the successful adaptation of the system to maintain the vitality of single cells during and after manipulation. In this context, the influences of the microfluidic environment as well as the applied electric fields on the vitality of the cells and the cytosolic Ca2+ concentration as crucially important physiological parameters were thoroughly investigated. While a short-term DEP manipulation did not affect the vitality of the cells, they showed irregular Ca2+ transients upon exposure to the DEP field only. The rate and the strength of these Ca2+ signals depended on exposure time, electric field strength and field frequency. By minimizing their occurrence rate, experimental conditions were identified that caused the least interference with the physiology of the cell. The possibility to precisely control the exact time point of stimulus application, to simultaneously analyze short-term reactions and to correlate them with later events of the signal transduction cascade on the level of individual cells makes this approach unique among previously described applications and offers new possibilities to unravel the mechanisms underlying intercellular communication.
N2  - Zelluläre Interaktionen sind wirkungsvolle Mechanismen zur Kontrolle zellulärer Zustände in vivo. Für die Entschlüsselung der dabei beteiligten Signaltransduktionsprozesse müssen definierte Ereignisse entlang der zellulären Signalkaskade erfasst und ihre wechselseitige Beziehung zueinander aufgeklärt werden. Dies kann von Ensemble-Messungen nicht geleistet werden, da die Mittelung biologischer Daten die Variabilität des Antwortverhaltens individueller Zellen missachtet und verschwommene Resultate liefert. Nur eine Multiparameteranalyse auf Einzelzellebene kann die entscheidenden Informationen liefern, die für ein detailliertes Verständnis zellulärer Signalwege unabdingbar sind. Ziel der vorliegenden Arbeit war die Entwicklung einer Methode, welche die gezielte Kontaktierung einzelner Zellen mit anderen Zellen oder Partikeln ermöglicht und mit der die dadurch ausgelösten zellulären Reaktionen auf unterschiedlichen zeitlichen Ebenen analysiert und miteinander korreliert werden können. Da dies die schonende Handhabung einzeln adressierbarer Zellen erfordert, wurde ein auf Dielektrophorese (DEP) basierendes mikrofluidisches System eingesetzt, welches die berührungslose Manipulation mikroskaliger Objekte mit hoher zeitlicher und örtlicher Präzision erlaubt. Das System besitzt ein hohes Potential zur Automatisierung und Parallelisierung, was für eine robuste und reproduzierbare Analyse lebender Zellen essentiell, und daher eine wichtige Voraussetzung für eine Anwendung in der Biomedizin ist. Als Modellsystem für interzelluläre Kommunikation wurde die T-Zell-Aktivierung gewählt. Die Aktivierung der einzelnen T-Zellen wurde durch ihre gezielte Kontaktierung mit Mikropartikeln („beads“) induziert, welche mit Antikörpern gegen spezielle Oberflächenproteine, wie die dem T-Zell-Rezeptor assoziierte Kinase CD3 oder das kostimulatorische Protein CD28, beschichtet waren. Die Stimulation der Zellen mit den funktionalisierten beads führte zu einem raschen Anstieg der intrazellulären Ca2+-Konzentration, welche über eine ratiometrische Detektion des Ca2+-sensitiven Fluoreszenzfarbstoffs Fura-2 gemessen wurde. Anschließend wurden die einzelnen Zellen aus dem mikrofluidischen System isoliert und weiterkultiviert. Am nächsten Tag wurden Zellteilung und die CD69-Expression – ein wichtiger Marker für aktivierte T-Zellen – analysiert und auf Ebene der individuellen Zelle mit dem zuvor gemessenen Ca2+-Signal korreliert. Es stellte sich heraus, dass der zeitliche Verlauf des intrazellulären Ca2+-Signals zwischen aktivierten und nicht aktivierten, sowie zwischen geteilten und nicht geteilten Zellen signifikant verschieden war. Dies zeigt, dass Ca2+-Signale in stimulierten T-Zellen wichtige Informationen über eine spätere Reaktion der Zelle liefern können. Da Einzelzellen äußerst empfindlich auf ihre Umgebungsbedingungen reagieren, war die Anpassung der experimentellen Vorgehensweise im Hinblick auf die Zellverträglichkeit von großer Bedeutung. Vor diesem Hintergrund wurde der Einfluss sowohl der mikrofluidischen Umgebung, als auch der elektrischen Felder auf die Überlebensrate und die intrazelluläre Ca2+-Konzentration der Zellen untersucht. Während eine kurzzeitige DEP-Manipulation im mikrofluidischen System die Vitalität der Zellen nicht beeinträchtigte, zeigten diese unregelmäßige Fluktuationen ihrer intrazellulären Ca2+-Konzentration selbst bei geringer elektrischer Feldexposition. Die Ausprägung dieser Fluktuationen war abhängig von der Expositionszeit, der elektrischen Feldstärke und der Feldfrequenz. Über die Minimierung ihres Auftretens konnten experimentelle Bedingungen mit dem geringsten Einfluss auf die Physiologie der Zellen identifiziert werden. Die Möglichkeit, einzelne Zellen zeitlich definiert und präzise mit anderen Zellen oder Oberflächen zu kontaktieren, die unmittelbare Reaktion der Zellen zu messen und diese mit späteren Ereignissen der Zellantwort zu korrelieren, macht die hier vorgestellte Methode einzigartig im Vergleich mit anderen Ansätzen und eröffnet neue Wege, die der interzellulären Kommunikation zugrunde liegenden Mechanismen aufzuklären.
KW  - T-Zell Aktivierung
KW  - Calcium
KW  - Einzelzellen
KW  - Mikrofluidik
KW  - Dielektrophorese
KW  - T cell activation
KW  - calcium
KW  - single-cell
KW  - lab on a chip
KW  - dielectrophoresis
Y1  - 2009
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-39576
ER  - 
TY  - THES
A1  - Gerling, Marten Tobias
T1  - A microfluidic system for high-precision image-based live cell sorting using dielectrophoretic forces
T1  - Ein mikrofluidisches System zur hochpräzisen und bildgestützten Sortierung lebender Zellen mittels dielektrophoretischer Kräfte
N2  - An important goal in biotechnology and (bio-) medical research is the isolation of single cells from a heterogeneous cell population. These specialised cells are of great interest for bioproduction, diagnostics, drug development, (cancer) therapy and research. To tackle emerging questions, an ever finer differentiation between target cells and non-target cells is required. This precise differentiation is a challenge for a growing number of available methods.
Since the physiological properties of the cells are closely linked to their morphology, it is beneficial to include their appearance in the sorting decision. For established methods, this represents a non addressable parameter, requiring new methods for the identification and isolation of target cells. Consequently, a variety of new flow-based methods have been developed and presented in recent years utilising 2D imaging data to identify target cells within a sample. As these methods aim for high throughput, the devices developed typically require highly complex fluid handling techniques, making them expensive while offering limited image quality.
In this work, a new continuous flow system for image-based cell sorting was developed that uses dielectrophoresis to precisely handle cells in a microchannel. Dielectrophoretic forces are exerted by inhomogeneous alternating electric fields on polarisable particles (here: cells). In the present system, the electric fields can be switched on and off precisely and quickly by a signal generator. In addition to the resulting simple and effective cell handling, the system is characterised by the outstanding quality of the image data generated and its compatibility with standard microscopes. These aspects result in low complexity, making it both affordable and user-friendly.
With the developed cell sorting system, cells could be sorted reliably and efficiently according to their cytosolic staining as well as morphological properties at different optical magnifications. The achieved purity of the target cell population was up to 95% and about 85% of the sorted cells could be recovered from the system. Good agreement was achieved between the results obtained and theoretical considerations. The achieved throughput of the system was up to 12,000 cells per hour. Cell viability studies indicated a high biocompatibility of the system.
The results presented demonstrate the potential of image-based cell sorting using dielectrophoresis. The outstanding image quality and highly precise yet gentle handling of the cells set the system apart from other technologies. This results in enormous potential for processing valuable and sensitive cell samples.
N2  - Ein wichtiges Ziel in der Biotechnologie und (bio-) medizinischen Forschung ist die Isolation von Einzelzellen aus einer heterogenen Zellpopulation. Aufgrund ihrer besonderen Eigenschaften sind diese Zellen für die Bioproduktion, Diagnostik, Arzneimittelentwicklung, (Krebs-) Therapie und Forschung von großem Interesse. Um neue Fragestellungen angehen zu können, ist eine immer feinere Differenzierung zwischen Zielzellen und Nicht-Zielzellen erforderlich. Diese präzise Differenzierung stellt eine Herausforderung für eine wachsende Zahl verfügbarer Methoden dar.

Da die physiologischen Eigenschaften der Zellen eng mit ihrer Morphologie verknüpft sind, ist es sinnvoll ihr Erscheinungsbild mit in die Sortierentscheidung einzubeziehen. Für etablierte Methoden stellt dies jedoch einen nicht adressierbaren Parameter dar, weshalb neue Methoden zur Identifikation und Isolation der Zielzellen benötigt werden. Folglich wurde in den letzten Jahren eine Vielzahl neuer durchflussbasierter Methoden entwickelt und vorgestellt, die 2D-Bilddaten zur Identifikation der Zielzellen innerhalb einer Probe heranziehen. Da diese Methoden auf hohe Durchsätze abzielen, erfordern die entwickelten Geräte in der Regel hochkomplexe Techniken zur Handhabung der Flüssigkeiten, was sie teuer macht und gleichzeitig zu einer begrenzten Bildqualität führt.

In dieser Arbeit wurde ein neues durchflussbasiertes System zur bildbasierten Zellsortierung entwickelt, das Dielektrophorese zur präzisen Handhabung der Zellen in einem Mikrokanal verwendet. Dielektrophoretische Kräfte werden von inhomogenen elektrischen Wechselfeldern auf polarisierbare Partikel (hier: Zellen) ausgeübt. Bei dem vorliegenden System können die elektrischen Felder durch einen Signalgenerator präzise und schnell ein- und ausgeschaltet werden. Neben der daraus resultierenden einfachen und effektiven Handhabung der Zellen zeichnet sich das System durch die hervorragende Qualität der erzeugten Bilddaten und die Kompatibilität mit Standardmikroskopen aus. Diese Aspekte führen zu einer geringen Komplexität, die es sowohl erschwinglich als auch benutzerfreundlich macht.

Mit dem entwickelten System zur Zellsortierung konnten Zellen sowohl auf Basis einer zytosolischen Färbung als auch auf Basis morphologischer Eigenschaften bei verschiedenen optischen Vergrößerungen zuverlässig und effizient sortiert werden. Die erreichte Reinheit der Zielzellpopulation betrug bis zu 95% wobei etwa 85% der sortierten Zellen aus dem System zurückgewonnen werden konnten. Dabei wurde eine gute Übereinstimmung der ermittelten Ergebnisse mit theoretischen Überlegungen erreicht. Der erreichte Durchsatz des Systems betrug bis zu 12.000 Zellen pro Stunde. Untersuchungen der Zellvitalität deuteten darauf hin, dass das System eine hohe Biokompatibilität aufweist.

Die vorgestellten Ergebnisse demonstrieren das Potenzial der bildbasierten Zellsortierung mittels Dielektrophorese. Die herausragende Bildqualität und hochpräzise aber dennoch zellschonende Handhabung der Zellen grenzen das System von anderen Technologien ab. Daraus ergibt sich ein enormes Potenzial für die Verarbeitung wertvoller und sensibler Zellproben.
KW  - microfluidics
KW  - cell sorting
KW  - dielectrophoresis
KW  - Zellsortierung
KW  - Dielektrophorese
KW  - Mikrofluidik
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-587421
ER  - 
TY  - GEN
A1  - Krupinski, Pawel
A1  - Bozorg, Behruz
A1  - Larsson, André
A1  - Pietra, Stefano
A1  - Grebe, Markus
A1  - Jönsson, Henrik
T1  - A model analysis of mechanisms for radial microtubular patterns at root hair initiation sites
T2  - Frontiers in plant science
N2  - Plant cells have two main modes of growth generating anisotropic structures. Diffuse growth where whole cell walls extend in specific directions, guided by anisotropically positioned cellulose fibers, and tip growth, with inhomogeneous addition of new cell wall material at the tip of the structure. Cells are known to regulate these processes via molecular signals and the cytoskeleton. Mechanical stress has been proposed to provide an input to the positioning of the cellulose fibers via cortical microtubules in diffuse growth. In particular, a stress feedback model predicts a circumferential pattern of fibers surrounding apical tissues and growing primordia, guided by the anisotropic curvature in such tissues. In contrast, during the initiation of tip growing root hairs, a star-like radial pattern has recently been observed. Here, we use detailed finite element models to analyze how a change in mechanical properties at the root hair initiation site can lead to star-like stress patterns in order to understand whether a stress-based feedback model can also explain the microtubule patterns seen during root hair initiation. We show that two independent mechanisms, individually or combined, can be sufficient to generate radial patterns. In the first, new material is added locally at the position of the root hair. In the second, increased tension in the initiation area provides a mechanism. Finally, we describe how a molecular model of Rho-of-plant (ROP) GTPases activation driven by auxin can position a patch of activated ROP protein basally along a 2D root epidermal cell plasma membrane, paving the way for models where mechanical and molecular mechanisms cooperate in the initial placement and outgrowth of root hairs.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 435 
KW  - plant cell wall
KW  - finite element modeling
KW  - computational morphodynamics
KW  - root hair initiation
KW  - microtubules
KW  - cellulose fibers
KW  - composite material
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407181
ER  - 
TY  - JOUR
A1  - Winkelbeiner, Nicola Lisa
A1  - Wandt, Viktoria Klara Veronika
A1  - Ebert, Franziska
A1  - Lossow, Kristina
A1  - Bankoglu, Ezgi E.
A1  - Martin, Maximilian
A1  - Mangerich, Aswin
A1  - Stopper, Helga
A1  - Bornhorst, Julia
A1  - Kipp, Anna Patricia
A1  - Schwerdtle, Tanja
T1  - A Multi-Endpoint Approach to Base Excision Repair Incision Activity Augmented by PARylation and DNA Damage Levels in Mice
BT  - Impact of Sex and Age
JF  - International Journal of Molecular Sciences
N2  - Investigation of processes that contribute to the maintenance of genomic stability is one crucial factor in the attempt to understand mechanisms that facilitate ageing. The DNA damage response (DDR) and DNA repair mechanisms are crucial to safeguard the integrity of DNA and to prevent accumulation of persistent DNA damage. Among them, base excision repair (BER) plays a decisive role. BER is the major repair pathway for small oxidative base modifications and apurinic/apyrimidinic (AP) sites. We established a highly sensitive non-radioactive assay to measure BER incision activity in murine liver samples. Incision activity can be assessed towards the three DNA lesions 8-oxo-2’-deoxyguanosine (8-oxodG), 5-hydroxy-2’-deoxyuracil (5-OHdU), and an AP site analogue. We applied the established assay to murine livers of adult and old mice of both sexes. Furthermore, poly(ADP-ribosyl)ation (PARylation) was assessed, which is an important determinant in DDR and BER. Additionally, DNA damage levels were measured to examine the overall damage levels. No impact of ageing on the investigated endpoints in liver tissue were found. However, animal sex seems to be a significant impact factor, as evident by sex-dependent alterations in all endpoints investigated. Moreover, our results revealed interrelationships between the investigated endpoints indicative for the synergetic mode of action of the cellular DNA integrity maintaining machinery.
KW  - maintenance of genomic integrity
KW  - ageing
KW  - sex
KW  - DNA damage
KW  - base excision repair (incision activity)
KW  - DNA damage response
KW  - poly(ADP-ribosyl)ation
KW  - liver
Y1  - 2020
U6  - https://doi.org/10.3390/ijms21186600
SN  - 1422-0067
VL  - 21
IS  - 18
PB  - Molecular Diversity Preservation International
CY  - Basel
ER  - 
TY  - GEN
A1  - Winkelbeiner, Nicola Lisa
A1  - Wandt, Viktoria Klara Veronika
A1  - Ebert, Franziska
A1  - Lossow, Kristina
A1  - Bankoglu, Ezgi E.
A1  - Martin, Maximilian
A1  - Mangerich, Aswin
A1  - Stopper, Helga
A1  - Bornhorst, Julia
A1  - Kipp, Anna Patricia
A1  - Schwerdtle, Tanja
T1  - A Multi-Endpoint Approach to Base Excision Repair Incision Activity Augmented by PARylation and DNA Damage Levels in Mice
BT  - Impact of Sex and Age
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - Investigation of processes that contribute to the maintenance of genomic stability is one crucial factor in the attempt to understand mechanisms that facilitate ageing. The DNA damage response (DDR) and DNA repair mechanisms are crucial to safeguard the integrity of DNA and to prevent accumulation of persistent DNA damage. Among them, base excision repair (BER) plays a decisive role. BER is the major repair pathway for small oxidative base modifications and apurinic/apyrimidinic (AP) sites. We established a highly sensitive non-radioactive assay to measure BER incision activity in murine liver samples. Incision activity can be assessed towards the three DNA lesions 8-oxo-2’-deoxyguanosine (8-oxodG), 5-hydroxy-2’-deoxyuracil (5-OHdU), and an AP site analogue. We applied the established assay to murine livers of adult and old mice of both sexes. Furthermore, poly(ADP-ribosyl)ation (PARylation) was assessed, which is an important determinant in DDR and BER. Additionally, DNA damage levels were measured to examine the overall damage levels. No impact of ageing on the investigated endpoints in liver tissue were found. However, animal sex seems to be a significant impact factor, as evident by sex-dependent alterations in all endpoints investigated. Moreover, our results revealed interrelationships between the investigated endpoints indicative for the synergetic mode of action of the cellular DNA integrity maintaining machinery.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1021 
KW  - maintenance of genomic integrity
KW  - ageing
KW  - sex
KW  - DNA damage
KW  - base excision repair (incision activity)
KW  - DNA damage response
KW  - poly(ADP-ribosyl)ation
KW  - liver
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-484831
SN  - 1866-8372
IS  - 1021
ER  - 
TY  - GEN
A1  - Sarauli, David
A1  - Xu, Chenggang
A1  - Dietzel, Birgit
A1  - Schulz, Burkhard
A1  - Lisdat, Fred
T1  - A multilayered sulfonated polyaniline network with entrapped pyrroloquinoline quinone-dependent glucose dehydrogenase
BT  - tunable direct bioelectrocatalysis
N2  - A feasible approach to construct multilayer films of sulfonated polyanilines – PMSA1 and PABMSA1 – containing different ratios of aniline, 2-methoxyaniline-5-sulfonic acid (MAS) and 3-aminobenzoic acid (AB), with the entrapped redox enzyme pyrroloquinoline quinone-dependent glucose dehydrogenase (PQQ-GDH) on Au and ITO electrode surfaces, is described. The formation of layers has been followed and confirmed by electrochemical impedance spectroscopy (EIS), which demonstrates that the multilayer assembly can be achieved in a progressive and uniform manner. The gold and ITO electrodes subsequently modified with PMSA1:PQQ-GDH and PABMSA1 films are studied by cyclic voltammetry (CV) and UV-Vis spectroscopy which show a significant direct bioelectrocatalytical response to the oxidation of the substrate glucose without any additional mediator. This response correlates linearly with the number of deposited layers. Furthermore, the constructed polymer/enzyme multilayer system exhibits a rather good long-term stability, since the catalytic current response is maintained for more than 60% of the initial value even after two weeks of storage. This verifies that a productive interaction of the enzyme embedded in the film of substituted polyaniline can be used as a basis for the construction of bioelectronic units, which are useful as indicators for processes liberating glucose and allowing optical and electrochemical transduction.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 275 
Y1  - 2014
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-98744
ER  - 
TY  - JOUR
A1  - Cheng, Feng
A1  - Dennis, Alice B.
A1  - Osuoha, Josephine Ijeoma
A1  - Canitz, Julia
A1  - Kirschbaum, Frank
A1  - Tiedemann, Ralph
T1  - A new genome assembly of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha
JF  - BMC genomics
N2  - Background
Teleost fishes comprise more than half of the vertebrate species. Within teleosts, most phylogenies consider the split between Osteoglossomorpha and Euteleosteomorpha/Otomorpha as basal, preceded only by the derivation of the most primitive group of teleosts, the Elopomorpha. While Osteoglossomorpha are generally species poor, the taxon contains the African weakly electric fish (Mormyroidei), which have radiated into numerous species. Within the mormyrids, the genus Campylomormyrus is mostly endemic to the Congo Basin. Campylomormyrus serves as a model to understand mechanisms of adaptive radiation and ecological speciation, especially with regard to its highly diverse species-specific electric organ discharges (EOD). Currently, there are few well-annotated genomes available for electric fish in general and mormyrids in particular. Our study aims at producing a high-quality genome assembly and to use this to examine genome evolution in relation to other teleosts. This will facilitate further understanding of the evolution of the osteoglossomorpha fish in general and of electric fish in particular.

Results
A high-quality weakly electric fish (C. compressirostris) genome was produced from a single individual with a genome size of 862 Mb, consisting of 1,497 contigs with an N50 of 1,399 kb and a GC-content of 43.69%. Gene predictions identified 34,492 protein-coding genes, which is a higher number than in the two other available Osteoglossomorpha genomes of Paramormyrops kingsleyae and Scleropages formosus. A Computational Analysis of gene Family Evolution (CAFE5) comparing 33 teleost fish genomes suggests an overall faster gene family turnover rate in Osteoglossomorpha than in Otomorpha and Euteleosteomorpha. Moreover, the ratios of expanded/contracted gene family numbers in Osteoglossomorpha are significantly higher than in the other two taxa, except for species that had undergone an additional genome duplication (Cyprinus carpio and Oncorhynchus mykiss). As potassium channel proteins are hypothesized to play a key role in EOD diversity among species, we put a special focus on them, and manually curated 16 Kv1 genes. We identified a tandem duplication in the KCNA7a gene in the genome of C. compressirostris. 

Conclusions
We present the fourth genome of an electric fish and the third well-annotated genome for Osteoglossomorpha, enabling us to compare gene family evolution among major teleost lineages. Osteoglossomorpha appear to exhibit rapid gene family evolution, with more gene family expansions than contractions. The curated Kv1 gene family showed seven gene clusters, which is more than in other analyzed fish genomes outside Osteoglossomorpha. The KCNA7a, encoding for a potassium channel central for EOD production and modulation, is tandemly duplicated which may related to the diverse EOD observed among Campylomormyrus species.
KW  - Campylomormyrus
KW  - Pacbio sequencing
KW  - Gene family
KW  - Osteoglossomorpha
KW  - Kv1
Y1  - 2023
U6  - https://doi.org/10.1186/s12864-023-09196-6
SN  - 1471-2164
VL  - 24
IS  - 1
PB  - BMC
CY  - London
ER  - 
TY  - GEN
A1  - Obbard, Darren J.
A1  - Shi, Mang
A1  - Roberts, Katherine E.
A1  - Longdon, Ben
A1  - Dennis, Alice B.
T1  - A new lineage of segmented RNA viruses infecting animals
T2  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1411 
KW  - metagenome
KW  - RNA virus
KW  - dark virus
KW  - arthropod
KW  - RNA interference
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-516040
SN  - 1866-8372
IS  - 1
ER  - 
TY  - JOUR
A1  - Obbard, Darren J.
A1  - Shi, Mang
A1  - Roberts, Katherine E.
A1  - Longdon, Ben
A1  - Dennis, Alice B.
T1  - A new lineage of segmented RNA viruses infecting animals
JF  - Virus Evolution
N2  - Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.
KW  - metagenome
KW  - RNA virus
KW  - dark virus
KW  - arthropod
KW  - RNA interference
Y1  - 2020
U6  - https://doi.org/10.1093/ve/vez061
SN  - 2057-1577
VL  - 6
IS  - 1
SP  - 1
EP  - 10
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - GEN
A1  - Kocyan, Alexander
A1  - Wiland-Szymanska, Justyna
T1  - A new name and a new combination for Friedmannia nom. illeg. (Hypoxidaceae)
T2  - Phytotaxa : a rapid international journal for accelerating the publication of botanical taxonomy
N2  - Recently, Kocyan & Wiland-Szymańska (2016) have published a thorough research article on one of the outstanding members of the family Hypoxidaceae on the Seychelles, which resulted in the raise of a new genus (Friedmannia Kocyan & Wiland-Szymańska 2016: 60) to accommodate the former Curculigo seychellensis Bojer ex Baker (1877: 368). However, it has turned out that the name Friedmannia Chantanachat & Bold (1962: 45) already exists in literature for a green alga, which renders the new hypoxid genus illegitimate (Melbourne Code; McNeill et al. 2012). Therefore, we assign a new generic epithet to Curculigo seychellensis.
Y1  - 2017
U6  - https://doi.org/10.11646/phytotaxa.291.3.10
SN  - 1179-3155
SN  - 1179-3163
VL  - 291
IS  - 3
SP  - 239
EP  - 239
PB  - Magnolia Press
CY  - Auckland
ER  - 
TY  - JOUR
A1  - Van den Wyngaert, Silke
A1  - Seto, Kensuke
A1  - Rojas-Jimenez, Keilor
A1  - Kagami, Maiko
A1  - Grossart, Hans-Peter
T1  - A New Parasitic Chytrid, Staurastromyces oculus (Rhizophydiales, Staurastromy-cetaceae fam. nov.), Infecting the Freshwater Desmid Staurastrum sp.
JF  - Protist
N2  - Chytrids are a diverse group of ubiquitous true zoosporic fungi. The recent molecular discovery of a large diversity of undescribed chytrids has raised awareness on their important, but so far understudied ecological role in aquatic ecosystems. In the pelagic zone, of both freshwater and marine ecosystems, many chytrid species have been morphologically described as parasites on almost all major groups of phytoplankton. However, the majority of these parasitic chytrids has rarely been isolated and lack DNA sequence data, resulting in a large proportion of "dark taxa" in databases. Here, we report on the isolation and in-depth morphological, molecular and host range characterization of a chytrid infecting the common freshwater desmid Staurastrum sp. We provide first insights on the metabolic activity of the different chytrid development stages by using the vital dye FUN (R)-1 (2-chloro-4-[2,3-dihydro-3-methyl-[benzo-1,3-thiazol-2-yl]-methylidene]-1-phenylquinolinium iodide). Cross infection experiments suggest that this chytrid is an obligate parasite and specific for the genus Staurastrum sp. Phylogenetic analysis, based on ITS1-5.8S-ITS2 and 28S rDNA sequences, placed it in the order Rhizophydiales. Based on the unique zoospore ultrastructure, combined with thallus morphology, and molecular phylogenetic placement, we describe this parasitic chytrid as a new genus and species Staurastromyces oculus, within a new family Staurastromycetaceae. (C) 2017 Elsevier GmbH. All rights reserved.
KW  - Chytrids
KW  - parasite
KW  - phytoplankton
KW  - Staurastromyces oculus
KW  - Staurastrum sp.
Y1  - 2017
U6  - https://doi.org/10.1016/j.protis.2017.05.001
SN  - 1434-4610
VL  - 168
SP  - 392
EP  - 407
PB  - Elsevier
CY  - Jena
ER  - 
TY  - GEN
A1  - Göthel, Markus
A1  - Listek, Martin
A1  - Messerschmidt, Katrin
A1  - Schlör, Anja
A1  - Hönow, Anja
A1  - Hanack, Katja
T1  - A New Workflow to Generate Monoclonal Antibodies against Microorganisms
T2  - Mathematisch-Naturwissenschaftliche Reihe
N2  - Monoclonal antibodies are used worldwide as highly potent and efficient detection reagents for research and diagnostic applications. Nevertheless, the specific targeting of complex antigens such as whole microorganisms remains a challenge. To provide a comprehensive workflow, we combined bioinformatic analyses with novel immunization and selection tools to design monoclonal antibodies for the detection of whole microorganisms. In our initial study, we used the human pathogenic strain E. coli O157:H7 as a model target and identified 53 potential protein candidates by using reverse vaccinology methodology. Five different peptide epitopes were selected for immunization using epitope-engineered viral proteins. The identification of antibody-producing hybridomas was performed by using a novel screening technology based on transgenic fusion cell lines. Using an artificial cell surface receptor expressed by all hybridomas, the desired antigen-specific cells can be sorted fast and efficiently out of the fusion cell pool. Selected antibody candidates were characterized and showed strong binding to the target strain E. coli O157:H7 with minor or no cross-reactivity to other relevant microorganisms such as Legionella pneumophila and Bacillus ssp. This approach could be useful as a highly efficient workflow for the generation of antibodies against microorganisms.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1174 
KW  - monoclonal antibody
KW  - antibody producing cell selection
KW  - hybridoma
KW  - epitope prediction
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-523341
SN  - 1866-8372
IS  - 20
ER  -