@article{CookLiCaietal.2019, author = {Cook, Katherine V. and Li, Chuang and Cai, Haiyuan and Krumholz, Lee R. and Hambright, K. David and Paerl, Hans W. and Steffen, Morgan M. and Wilson, Alan E. and Burford, Michele A. and Grossart, Hans-Peter and Hamilton, David P. and Jiang, Helong and Sukenik, Assaf and Latour, Delphine and Meyer, Elisabeth I. and Padisak, Judit and Qin, Boqiang and Zamor, Richard M. and Zhu, Guangwei}, title = {The global Microcystis interactome}, series = {Limnology and oceanography}, volume = {65}, journal = {Limnology and oceanography}, publisher = {Wiley}, address = {Hoboken}, issn = {0024-3590}, doi = {10.1002/lno.11361}, pages = {S194 -- S207}, year = {2019}, abstract = {Bacteria play key roles in the function and diversity of aquatic systems, but aside from study of specific bloom systems, little is known about the diversity or biogeography of bacteria associated with harmful cyanobacterial blooms (cyanoHABs). CyanoHAB species are known to shape bacterial community composition and to rely on functions provided by the associated bacteria, leading to the hypothesized cyanoHAB interactome, a coevolved community of synergistic and interacting bacteria species, each necessary for the success of the others. Here, we surveyed the microbiome associated with Microcystis aeruginosa during blooms in 12 lakes spanning four continents as an initial test of the hypothesized Microcystis interactome. We predicted that microbiome composition and functional potential would be similar across blooms globally. Our results, as revealed by 16S rRNA sequence similarity, indicate that M. aeruginosa is cosmopolitan in lakes across a 280 degrees longitudinal and 90 degrees latitudinal gradient. The microbiome communities were represented by a wide range of operational taxonomic units and relative abundances. Highly abundant taxa were more related and shared across most sites and did not vary with geographic distance, thus, like Microcystis, revealing no evidence for dispersal limitation. High phylogenetic relatedness, both within and across lakes, indicates that microbiome bacteria with similar functional potential were associated with all blooms. While Microcystis and the microbiome bacteria shared many genes, whole-community metagenomic analysis revealed a suite of biochemical pathways that could be considered complementary. Our results demonstrate a high degree of similarity across global Microcystis blooms, thereby providing initial support for the hypothesized Microcystis interactome.}, language = {en} } @article{ColomaGaedkeSivonenetal.2019, author = {Coloma, Sebastian and Gaedke, Ursula and Sivonen, Kaarina and Hiltunen, Teppo}, title = {Frequency of virus-resistant hosts determines experimental community dynamics}, series = {Ecology : a publication of the Ecological Society of America}, volume = {100}, journal = {Ecology : a publication of the Ecological Society of America}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {0012-9658}, doi = {10.1002/ecy.2554}, pages = {10}, year = {2019}, abstract = {Parasites, such as bacterial viruses (phages), can have large effects on host populations both at the ecological and evolutionary levels. In the case of cyanobacteria, phages can reduce primary production and infected hosts release intracellular nutrients influencing planktonic food web structure, community dynamics, and biogeochemical cycles. Cyanophages may be of great importance in aquatic food webs during large cyanobacterial blooms unless the host population becomes resistant to phage infection. The consequences on plankton community dynamics of the evolution of phage resistance in bloom forming cyanobacterial populations are still poorly studied. Here, we examined the effect of different frequencies of a phage-resistant genotype within a filamentous nitrogen-fixing Nodularia spumigena population on an experimental plankton community. Three Nodularia populations with different initial frequencies (0\%, 5\%, and 50\%) of phage-resistant genotypes were inoculated in separate treatments with the phage 2AV2, the green alga Chlorella vulgaris, and the rotifer Brachionus plicatilis, which formed the experimental plankton community subjected to either nitrogen-limited or nitrogen-rich conditions. We found that the frequency of the phage-resistant Nodularia genotype determined experimental community dynamics. Cyanobacterial populations with a high frequency (50\%) of the phage-resistant genotype dominated the cultures despite the presence of phages, retaining most of the intracellular nitrogen in the plankton community. In contrast, populations with low frequencies (0\% and 5\%) of the phage-resistant genotype were lysed and reduced to extinction by the phage, transferring the intracellular nitrogen held by Nodularia to Chlorella and rotifers, and allowing Chlorella to dominate the communities and rotifers to survive. This study shows that even though phages represent minuscule biomass, they can have key effects on community composition and eco-evolutionary feedbacks in plankton communities.}, language = {en} } @article{ColangeliSchlaegelOberteggeretal.2019, author = {Colangeli, Pierluigi and Schl{\"a}gel, Ulrike E. and Obertegger, Ulrike and Petermann, Jana S. and Tiedemann, Ralph and Weithoff, Guntram}, title = {Negative phototactic response to UVR in three cosmopolitan rotifers: a video analysis approach}, series = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, volume = {844}, journal = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {0018-8158}, doi = {10.1007/s10750-018-3801-y}, pages = {43 -- 54}, year = {2019}, language = {en} } @article{CoduttiBenteFaivreetal.2019, author = {Codutti, Agnese and Bente, Klaas and Faivre, Damien and Klumpp, Stefan}, title = {Chemotaxis in external fields: Simulations for active magnetic biological matter}, series = {PLoS Computational Biology : a new community journal}, volume = {15}, journal = {PLoS Computational Biology : a new community journal}, number = {12}, publisher = {PLoS}, address = {San Fransisco}, issn = {1553-734X}, doi = {10.1371/journal.pcbi.1007548}, pages = {26}, year = {2019}, abstract = {The movement of microswimmers is often described by active Brownian particle models. Here we introduce a variant of these models with several internal states of the swimmer to describe stochastic strategies for directional swimming such as run and tumble or run and reverse that are used by microorganisms for chemotaxis. The model includes a mechanism to generate a directional bias for chemotaxis and interactions with external fields (e.g., gravity, magnetic field, fluid flow) that impose forces or torques on the swimmer. We show how this modified model can be applied to various scenarios: First, the run and tumble motion of E. coli is used to establish a paradigm for chemotaxis and investigate how it is affected by external forces. Then, we study magneto-aerotaxis in magnetotactic bacteria, which is biased not only by an oxygen gradient towards a preferred concentration, but also by magnetic fields, which exert a torque on an intracellular chain of magnets. We study the competition of magnetic alignment with active reorientation and show that the magnetic orientation can improve chemotaxis and thereby provide an advantage to the bacteria, even at rather large inclination angles of the magnetic field relative to the oxygen gradient, a case reminiscent of what is expected for the bacteria at or close to the equator. The highest gain in chemotactic velocity is obtained for run and tumble with a magnetic field parallel to the gradient, but in general a mechanism for reverse motion is necessary to swim against the magnetic field and a run and reverse strategy is more advantageous in the presence of a magnetic torque. This finding is consistent with observations that the dominant mode of directional changes in magnetotactic bacteria is reversal rather than tumbles. Moreover, it provides guidance for the design of future magnetic biohybrid swimmers. Author summary In this paper, we propose a modified Active Brownian particle model to describe bacterial swimming behavior under the influence of external forces and torques, in particular of a magnetic torque. This type of interaction is particularly important for magnetic biohybrids (i.e. motile bacteria coupled to a synthetic magnetic component) and for magnetotactic bacteria (i.e. bacteria with a natural intracellular magnetic chain), which perform chemotaxis to swim along chemical gradients, but are also directed by an external magnetic field. The model allows us to investigate the benefits and disadvantages of such coupling between two different directionality mechanisms. In particular we show that the magnetic torque can speed chemotaxis up in some conditions, while it can hinder it in other cases. In addition to an understanding of the swimming strategies of naturally magnetotactic organisms, the results may guide the design of future biomedical devices.}, language = {en} } @article{ChenLiZhangetal.2019, author = {Chen, Shun-Gang and Li, Ji and Zhang, Fan and Xiao, Bo and Hu, Jia-Ming and Cui, Yin-Qiu and Hofreiter, Michael and Hou, Xin-Dong and Sheng, Gui-Lian and Lai, Xu-Long and Yuan, Jun-Xia}, title = {Different maternal lineages revealed by ancient mitochondrial genome of Camelus bactrianus from China}, series = {Mitochondrial DNA Part A}, volume = {30}, journal = {Mitochondrial DNA Part A}, number = {7}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {2470-1394}, doi = {10.1080/24701394.2019.1659250}, pages = {786 -- 793}, year = {2019}, abstract = {Domestic Bactrian camel (Camelus bactrianus) used to be one of the most important livestock species in Chinese history, as well as the major transport carrier on the ancient Silk Road. However, archeological studies on Chinese C. bactrianus are still limited, and molecular biology research on this species is mainly focused on modern specimens. In this study, we retrieved the complete mitochondrial genome from a C. bactrianus specimen, which was excavated from northwestern China and dated at 1290-1180 cal. Phylogenetic analyses using 18 mitochondrial genomes indicated that the C. bactrianus clade was divided into two maternal lineages. The majority of samples originating from Iran to Japan and Mongolia belong to subclade A1, while our sample together with two Mongolian individuals formed the much smaller subclade A2. Furthermore, the divergence time of these two maternal lineages was estimated as 165 Kya (95\% credibility interval 117-222 Kya), this might indicate that several different evolutionary lineages were incorporated into the domestic gene pool during the initial domestication process. Bayesian skyline plot (BSP) analysis a slow increase in female effective population size of C. bactrianus from 5000 years ago, which to the beginning of domestication of C. bactrianus. The present study also revealed that there were extensive exchanges of genetic information among C. bactrianus populations in regions along the Silk Road.}, language = {en} } @article{ChaturvediMehrotraKumarietal.2019, author = {Chaturvedi, Neha and Mehrotra, Bagish and Kumari, Sangeeta and Gupta, Saurabh and Subramanya, Hosahalli and Saberwal, Gayatri}, title = {Some data quality issues at ClinicalTrials.gov}, series = {Trials}, volume = {20}, journal = {Trials}, publisher = {BMC}, address = {London}, issn = {1745-6215}, doi = {10.1186/s13063-019-3408-2}, pages = {8}, year = {2019}, language = {en} } @article{ChapmanLantOhashietal.2019, author = {Chapman, Eric M. and Lant, Benjamin and Ohashi, Yota and Yu, Bin and Schertzberg, Michael and Go, Christopher and Dogra, Deepika and Koskimaki, Janne and Girard, Romuald and Li, Yan and Fraser, Andrew G. and Awad, Issam A. and Abdelilah-Seyfried, Salim and Gingras, Anne-Claude and Derry, William Brent}, title = {A conserved CCM complex promotes apoptosis non-autonomously by regulating zinc homeostasis}, series = {Nature Communications}, volume = {10}, journal = {Nature Communications}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/s41467-019-09829-z}, pages = {15}, year = {2019}, abstract = {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.}, language = {en} } @article{CastroFernandoReegetal.2019, author = {Castro, Jose Pedro and Fernando, Raquel and Reeg, Sandra and Meinl, Walter and Almeida, Henrique and Grune, Tilman}, title = {Non-enzymatic cleavage of Hsp90 by oxidative stress leads to actin aggregate formation}, series = {Redox Biology}, volume = {21}, journal = {Redox Biology}, publisher = {Elsevier}, address = {Amsterdam}, issn = {2213-2317}, doi = {10.1016/j.redox.2019.101108}, pages = {10}, year = {2019}, abstract = {Aging is accompanied by the accumulation of oxidized proteins. To remove them, cells employ the proteasomal and autophagy-lysosomal systems; however, if the clearance rate is inferior to its formation, protein aggregates form as a hallmark of proteostasis loss. In cells, during stress conditions, actin aggregates accumulate leading to impaired proliferation and reduced proteasomal activity, as observed in cellular senescence. The heat shock protein 90 (Hsp90) is a molecular chaperone that binds and protects the proteasome from oxidative inactivation. We hypothesized that in oxidative stress conditions a malfunction of Hsp90 occurs resulting in the aforementioned protein aggregates. Here, we demonstrate that upon oxidative stress Hsp90 loses its function in a highly specific non-enzymatic iron-catalyzed oxidation event and its breakdown product, a cleaved form of Hsp90 (Hsp90cl), acquires a new function in mediating the accumulation of actin aggregates. Moreover, the prevention of Hsp90 cleavage reduces oxidized actin accumulation, whereas transfection of the cleaved form of Hsp90 leads to an enhanced accumulation of oxidized actin. This indicates a clear role of the Hsp90cl in the aggregation of oxidized proteins.}, language = {en} } @article{BoertleinSchumacherKleuseretal.2019, author = {B{\"o}rtlein, Charlene and Schumacher, Fabian and Kleuser, Burkhard and D{\"o}lken, Lars and Avota, Elita}, title = {Role of Neutral Sphingomyelinase-2 (NSM 2) in the Control of T Cell Plasma Membrane Lipid Composition and Cholesterol Homeostasis}, series = {Frontiers in cell and developmental biology}, volume = {7}, journal = {Frontiers in cell and developmental biology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {2296-634X}, doi = {10.3389/fcell.2019.00226}, pages = {16}, year = {2019}, abstract = {The activity of neutral sphingomyelinase-2 (NSM2) to catalyze the conversion of sphingomyelin (SM) to ceramide and phosphocholine at the cytosolic leaflet of plasma membrane (PM) is important in T cell receptor (TCR) signaling. We recently identified PKC zeta as a major NSM2 downstream effector which regulates microtubular polarization. It remained, however, unclear to what extent NSM2 activity affected overall composition of PM lipids and downstream effector lipids in antigen stimulated T cells. Here, we provide a detailed lipidomics analyses on PM fractions isolated from TCR stimulated wild type and NSM2 deficient (Delta NSM) Jurkat T cells. This revealed that in addition to that of sphingolipids, NSM2 depletion also affected concentrations of many other lipids. In particular, NSM2 ablation resulted in increase of lyso-phosphatidylcholine (LPC) and lyso-phosphatidylethanolamine (LPE) which both govern PM biophysical properties. Crucially, TCR dependent upregulation of the important T cell signaling lipid diacylglycerol (DAG), which is fundamental for activation of conventional and novel PKCs, was abolished in Delta NSM cells. Moreover, NSM2 activity was found to play an important role in PM cholesterol transport to the endoplasmic reticulum (ER) and production of cholesteryl esters (CE) there. Most importantly, CE accumulation was essential to sustain human T cell proliferation. Accordingly, inhibition of CE generating enzymes, the cholesterol acetyltransferases ACAT1/SOAT1 and ACAT2/SOAT2, impaired TCR driven expansion of both CD4(+) and CD8(+) T cells. In summary, our study reveals an important role of NSM2 in regulating T cell functions by its multiple effects on PM lipids and cholesterol homeostasis.}, language = {en} } @article{BuschKlausSchaeferetal.2019, author = {Busch, Verena and Klaus, Valentin Helmut and Schaefer, Deborah and Prati, Daniel and Boch, Steffen and M{\"u}ller, J{\"o}rg and Chiste, Melanie and Mody, Karsten and Bl{\"u}thgen, Nico and Fischer, Markus and H{\"o}lzel, Norbert and Kleinebecker, Till}, title = {Will I stay or will I go? Plant species-specific response and tolerance to high land-use intensity in temperate grassland ecosystems}, series = {Journal of vegetation science}, volume = {30}, journal = {Journal of vegetation science}, number = {4}, publisher = {Wiley}, address = {Hoboken}, issn = {1100-9233}, doi = {10.1111/jvs.12749}, pages = {674 -- 686}, year = {2019}, language = {en} }