TY  - JOUR
A1  - Biscotti, Maria Assunta
A1  - Adolfi, Mateus Contar
A1  - Barucca, Marco
A1  - Forconi, Mariko
A1  - Pallavicini, Alberto
A1  - Gerdol, Marco
A1  - Canapa, Adriana
A1  - Schartl, Manfred
T1  - A comparative view on sex differentiation and gametogenesis genes in lungfish and coelacanths
JF  - Genome Biology and Evolution
N2  - Gonadal sex differentiation and reproduction are the keys to the perpetuation of favorable gene combinations and positively selected traits. In vertebrates, several gonad development features that differentiate tetrapods and fishes are likely to be, at least in part, related to the water-to-land transition. The collection of information from basal sarcopterygians, coelacanths, and lungfishes, is crucial to improve our understanding of the molecular evolution of pathways involved in reproductive functions, since these organisms are generally regarded as “living fossils” and as the direct ancestors of tetrapods. Here, we report for the first time the characterization of >50 genes related to sex differentiation and gametogenesis in Latimeria menadoensis and Protopterus annectens. Although the expression profiles of most genes is consistent with the intermediate position of basal sarcopterygians between actinopterygian fish and tetrapods, their phylogenetic placement and presence/absence patterns often reveal a closer affinity to the tetrapod orthologs. On the other hand, particular genes, for example, the male gonad factor gsdf (Gonadal Soma-Derived Factor), provide examples of ancestral traits shared with actinopterygians, which disappeared in the tetrapod lineage.
KW  - sex differentiation
KW  - Latimeria menadoensis
KW  - Protopterus annectens
KW  - evolution
KW  - testis
KW  - gametogenesis
KW  - ovary
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-176774
VL  - 10
IS  - 6
ER  - 
TY  - JOUR
A1  - Biltueva, Larisa S.
A1  - Prokopov, Dmitry Yu.
A1  - Romanenko, Svetlana A.
A1  - Interesova, Elena A.
A1  - Schartl, Manfred
A1  - Trifonov, Vladimir A.
T1  - Chromosome distribution of highly conserved tandemly arranged repetitive DNAs in the Siberian sturgeon (Acipenser baerii)
JF  - Genes
N2  - Polyploid genomes present a challenge for cytogenetic and genomic studies, due to the high number of similar size chromosomes and the simultaneous presence of hardly distinguishable paralogous elements. The karyotype of the Siberian sturgeon (Acipenser baerii) contains around 250 chromosomes and is remarkable for the presence of paralogs from two rounds of whole-genome duplications (WGD). In this study, we applied the sterlet-derived acipenserid satDNA-based whole chromosome-specific probes to analyze the Siberian sturgeon karyotype. We demonstrate that the last genome duplication event in the Siberian sturgeon was accompanied by the simultaneous expansion of several repetitive DNA families. Some of the repetitive probes serve as good cytogenetic markers distinguishing paralogous chromosomes and detecting ancestral syntenic regions, which underwent fusions and fissions. The tendency of minisatellite specificity for chromosome size groups previously observed in the sterlet genome is also visible in the Siberian sturgeon. We provide an initial physical chromosome map of the Siberian sturgeon genome supported by molecular markers. The application of these data will facilitate genomic studies in other recent polyploid sturgeon species.
KW  - Acipenser baerii
KW  - sturgeon karyotype
KW  - whole-genome duplication
KW  - paralogs
KW  - polyploidy
KW  - acipenserid minisatellite
KW  - satellite DNA
KW  - tandem repeats
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-219371
SN  - 2073-4425
VL  - 11
IS  - 11
ER  - 
TY  - JOUR
A1  - Biju, Joseph
A1  - Schwarz, Roland
A1  - Linke, Burkhard
A1  - Blom, Jochen
A1  - Becker, Anke
A1  - Claus, Heike
A1  - Goesmann, Alexander
A1  - Frosch, Matthias
A1  - Müller, Tobias
A1  - Vogel, Ulrich
A1  - Schoen, Christoph
T1  - Virulence Evolution of the Human Pathogen Neisseria meningitidis by Recombination in the Core and Accessory Genome
JF  - PLoS One
N2  - Background
Neisseria meningitidis is a naturally transformable, facultative pathogen colonizing the human nasopharynx. Here, we analyze on a genome-wide level the impact of recombination on gene-complement diversity and virulence evolution in N. meningitidis. We combined comparative genome hybridization using microarrays (mCGH) and multilocus sequence typing (MLST) of 29 meningococcal isolates with computational comparison of a subset of seven meningococcal genome sequences.

Principal Findings
We found that lateral gene transfer of minimal mobile elements as well as prophages are major forces shaping meningococcal population structure. Extensive gene content comparison revealed novel associations of virulence with genetic elements besides the recently discovered meningococcal disease associated (MDA) island. In particular, we identified an association of virulence with a recently described canonical genomic island termed IHT-E and a differential distribution of genes encoding RTX toxin- and two-partner secretion systems among hyperinvasive and non-hyperinvasive lineages. By computationally screening also the core genome for signs of recombination, we provided evidence that about 40% of the meningococcal core genes are affected by recombination primarily within metabolic genes as well as genes involved in DNA replication and repair. By comparison with the results of previous mCGH studies, our data indicated that genetic structuring as revealed by mCGH is stable over time and highly similar for isolates from different geographic origins.

Conclusions
Recombination comprising lateral transfer of entire genes as well as homologous intragenic recombination has a profound impact on meningococcal population structure and genome composition. Our data support the hypothesis that meningococcal virulence is polygenic in nature and that differences in metabolism might contribute to virulence.
KW  - population genetics
KW  - DNA recombination
KW  - meningococcal disease
KW  - recombinant proteins
KW  - genomic databases
KW  - comparative genomics
KW  - neisseria meningitidis
KW  - homologous recombination
Y1  - 2011
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-137960
VL  - 6
IS  - 4
ER  - 
TY  - JOUR
A1  - Biedermann, Peter H. W.
T1  - Cooperative Breeding in the Ambrosia Beetle Xyleborus affinis and Management of Its Fungal Symbionts
JF  - Frontiers in Ecology and Evolution
N2  - Fungus-farming is known from attine ants, macrotermites, and ambrosia beetles (Scolytinae, Platypodinae). Farming ant and termite societies are superorganismal and grow fungal cultivars in monocultures. Social organization of ambrosia beetle groups and their farming systems are poorly studied, because of their enigmatic life within tunnel systems inside of wood. Ambrosia beetle-fungus symbioses evolved many times independently in both the beetles and their fungal cultivars. Observations suggest that there is evolutionary convergence between these lineages, but also a high variation in the degree of sociality and the modes of fungiculture. Using a laboratory observation technique, I here tried to give insights into the social system and fungus symbiosis of the sugar-cane borer, Xyleborus affinis Eichhoff (Scolytinae: Curculionidae), a currently poorly studied ambrosia beetle. The study revealed a cooperatively breeding system characterized by delayed dispersal of adult daughters, alloparental brood care by larvae and adults, and about half of the totipotent adult daughters laying eggs within the natal nest. Most interesting, there was a tendency of egg-laying females to engage more commonly in mutually beneficial behaviors than non-egg-layers. Fungus gardens covering gallery walls composed of five different filamentous fungi. A Raffaelea isolate was predominant and together with an unidentified fungus likely served as the main food for adults and larvae. Three isolates, a Mucor, a Fusarium and a Phaeoacremonium isolate were most abundant in the oldest gallery part close to the entrance; Mucor, Fusarium and the Raffaelea isolate in diseased individuals. Additionally, there was correlative evidence for some fungal isoaltes influencing beetle feeding and hygienic behaviors. Overall, X. affinis is now the second ambrosia beetle that can be classified as a cooperative breeder with division of labor among and between adults and larvae.
KW  - cooperative breeding
KW  - bark beetle
KW  - insect agriculture
KW  - symbiosis
KW  - fungus community
KW  - social behavior
KW  - fungus-farming
KW  - mutualism
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-215662
SN  - 2296-701X
VL  - 8
ER  - 
TY  - JOUR
A1  - Bert, Bettina
A1  - Chmielewska, Justyna
A1  - Bergmann, Sven
A1  - Busch, Maximilian
A1  - Driever, Wolfgang
A1  - Finger-Baier, Karin
A1  - Hößler, Johanna
A1  - Köhler, Almut
A1  - Leich, Nora
A1  - Misgeld, Thomas
A1  - Nöldner, Torsten
A1  - Reiher, Annegret
A1  - Schartl, Manfred
A1  - Seebach-Sproedt, Anja
A1  - Thumberger, Thomas
A1  - Schönfelder, Gilbert
A1  - Grune, Barbara
T1  - Considerations for a European animal welfare standard to evaluate adverse phenotypes in teleost fish
JF  - The EMBO Journal
N2  - No abstract available.
KW  - Danio-rerio
KW  - Zebrafish
KW  - Pain
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-188783
VL  - 35
IS  - 11
ER  - 
TY  - JOUR
A1  - Bernards, R.
A1  - Schackleford, G. M.
A1  - Gerber, M. R.
A1  - Horowitz, J. M.
A1  - Friend, S. H.
A1  - Schartl, Manfred
A1  - Bogenmann, E.
A1  - Rapaport, J. M.
A1  - Mcgee, T.
A1  - Dryja, T. P.
T1  - Structure and expression of the murine retinoblastoma gene and characterization of its encoded protein
N2  - No abstract available
KW  - Physiologische Chemie
Y1  - 1989
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-61819
ER  - 
TY  - JOUR
A1  - Berberich, Andreas
A1  - Kurz, Andreas
A1  - Reinhard, Sebastian
A1  - Paul, Torsten Johann
A1  - Burd, Paul Ray
A1  - Sauer, Markus
A1  - Kollmannsberger, Philip
T1  - Fourier Ring Correlation and anisotropic kernel density estimation improve deep learning based SMLM reconstruction of microtubules
JF  - Frontiers in Bioinformatics
N2  - Single-molecule super-resolution microscopy (SMLM) techniques like dSTORM can reveal biological structures down to the nanometer scale. The achievable resolution is not only defined by the localization precision of individual fluorescent molecules, but also by their density, which becomes a limiting factor e.g., in expansion microscopy. Artificial deep neural networks can learn to reconstruct dense super-resolved structures such as microtubules from a sparse, noisy set of data points. This approach requires a robust method to assess the quality of a predicted density image and to quantitatively compare it to a ground truth image. Such a quality measure needs to be differentiable to be applied as loss function in deep learning. We developed a new trainable quality measure based on Fourier Ring Correlation (FRC) and used it to train deep neural networks to map a small number of sampling points to an underlying density. Smooth ground truth images of microtubules were generated from localization coordinates using an anisotropic Gaussian kernel density estimator. We show that the FRC criterion ideally complements the existing state-of-the-art multiscale structural similarity index, since both are interpretable and there is no trade-off between them during optimization. The TensorFlow implementation of our FRC metric can easily be integrated into existing deep learning workflows.
KW  - dSTORM
KW  - deep learning–artificial neural network (DL-ANN)
KW  - single molecule localization microscopy
KW  - microtubule cytoskeleton
KW  - super-resolution
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-261686
VL  - 1
ER  - 
TY  - JOUR
A1  - Benz, Roland
A1  - Maier, Elke
A1  - Bauer, Susanne
A1  - Ludwig, Albrecht
T1  - The Deletion of Several Amino Acid Stretches of Escherichia coli Alpha-Hemolysin (HlyA) Suggests That the Channel-Forming Domain Contains Beta-Strands
JF  - PLOS ONE
N2  - Escherichia coli α-hemolysin (HlyA) is a pore-forming protein of 110 kDa belonging to the family of RTX toxins. A hydrophobic region between the amino acid residues 238 and 410 in the N-terminal half of HlyA has previously been suggested to form hydrophobic and/or amphipathic α-helices and has been shown to be important for hemolytic activity and pore formation in biological and artificial membranes. The structure of the HlyA transmembrane channel is, however, largely unknown. For further investigation of the channel structure, we deleted in HlyA different stretches of amino acids that could form amphipathic β-strands according to secondary structure predictions (residues 71–110, 158–167, 180–203, and 264–286). These deletions resulted in HlyA mutants with strongly reduced hemolytic activity. Lipid bilayer measurements demonstrated that HlyAΔ71–110 and HlyAΔ264–286 formed channels with much smaller single-channel conductance than wildtype HlyA, whereas their channel-forming activity was virtually as high as that of the wildtype toxin. HlyAΔ158–167 and HlyAΔ180–203 were unable to form defined channels in lipid bilayers. Calculations based on the single-channel data indicated that the channels generated by HlyAΔ71–110 and HlyAΔ264–286 had a smaller size (diameter about 1.4 to 1.8 nm) than wildtype HlyA channels (diameter about 2.0 to 2.6 nm), suggesting that in these mutants part of the channel-forming domain was removed. Osmotic protection experiments with erythrocytes confirmed that HlyA, HlyAΔ71–110, and HlyAΔ264–286 form defined transmembrane pores and suggested channel diameters that largely agreed with those estimated from the single-channel data. Taken together, these results suggest that the channel-forming domain of HlyA might contain β-strands, possibly in addition to α-helical structures.
KW  - membrane potential
KW  - molecular mass
KW  - cations
KW  - membrane structures
KW  - membrane proteins
KW  - lipid bilayer
KW  - red blood cells
KW  - toxins
Y1  - 2014
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-118115
SN  - 1932-6203
VL  - 9
IS  - 12
ER  - 
TY  - JOUR
A1  - Bensaad, Karim
A1  - Favaro, Elena
A1  - Lewis, Caroline A.
A1  - Peck, Barrie
A1  - Lord, Simon
A1  - Collins, Jennifer M.
A1  - Pinnick, Katherine E.
A1  - Wigfield, Simon
A1  - Buffa, Francesca M.
A1  - Li, Ji-Liang
A1  - Zhang, Qifeng
A1  - Wakelam, Michael J. O.
A1  - Karpe, Fredrik
A1  - Schulze, Almut
A1  - Harris, Adrian L.
T1  - Fatty Acid Uptake and Lipid Storage Induced by HIF-1 alpha Contribute to Cell Growth and Survival after Hypoxia-Reoxygenation
JF  - Cell Reports
N2  - An in vivo model of antiangiogenic therapy allowed us to identify genes upregulated by bevacizumab treatment, including Fatty Acid Binding Protein 3 (FABP3) and FABP7, both of which are involved in fatty acid uptake. In vitro, both were induced by hypoxia in a hypoxia-inducible factor-1 alpha (HIF-1 alpha)-dependent manner. There was a significant lipid droplet (LD) accumulation in hypoxia that was time and O-2 concentration dependent. Knockdown of endogenous expression of FABP3, FABP7, or Adipophilin (an essential LD structural component) significantly impaired LD formation under hypoxia. We showed that LD accumulation is due to FABP3/7-dependent fatty acid uptake while de novo fatty acid synthesis is repressed in hypoxia. We also showed that ATP production occurs via beta-oxidation or glycogen degradation in a cell-type-dependent manner in hypoxia-reoxygenation. Finally, inhibition of lipid storage reduced protection against reactive oxygen species toxicity, decreased the survival of cells subjected to hypoxia-reoxygenation in vitro, and strongly impaired tumorigenesis in vivo.
KW  - inducible factor-I
KW  - binding protein
KW  - triglyceride accumulation
KW  - cancer cell
KW  - complex-III
KW  - beta-oxidation
KW  - metabolism
KW  - lipogenesis
KW  - proliferation
KW  - resistance
Y1  - 2014
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-115162
SN  - 2211-1247
VL  - 9
IS  - 1
ER  - 
TY  - JOUR
A1  - Benoit, Joshua B.
A1  - Adelman, Zach N.
A1  - Reinhardt, Klaus
A1  - Dolan, Amanda
A1  - Poelchau, Monica
A1  - Jennings, Emily C.
A1  - Szuter, Elise M.
A1  - Hagan, Richard W.
A1  - Gujar, Hemant
A1  - Shukla, Jayendra Nath
A1  - Zhu, Fang
A1  - Mohan, M.
A1  - Nelson, David R.
A1  - Rosendale, Andrew J.
A1  - Derst, Christian
A1  - Resnik, Valentina
A1  - Wernig, Sebastian
A1  - Menegazzi, Pamela
A1  - Wegener, Christian
A1  - Peschel, Nicolai
A1  - Hendershot, Jacob M.
A1  - Blenau, Wolfgang
A1  - Predel, Reinhard
A1  - Johnston, Paul R.
A1  - Ioannidis, Panagiotis
A1  - Waterhouse, Robert M.
A1  - Nauen, Ralf
A1  - Schorn, Corinna
A1  - Ott, Mark-Christoph
A1  - Maiwald, Frank
A1  - Johnston, J. Spencer
A1  - Gondhalekar, Ameya D.
A1  - Scharf, Michael E.
A1  - Raje, Kapil R.
A1  - Hottel, Benjamin A.
A1  - Armisén, David
A1  - Crumière, Antonin Jean Johan
A1  - Refki, Peter Nagui
A1  - Santos, Maria Emilia
A1  - Sghaier, Essia
A1  - Viala, Sèverine
A1  - Khila, Abderrahman
A1  - Ahn, Seung-Joon
A1  - Childers, Christopher
A1  - Lee, Chien-Yueh
A1  - Lin, Han
A1  - Hughes, Daniel S.T.
A1  - Duncan, Elizabeth J.
A1  - Murali, Shwetha C.
A1  - Qu, Jiaxin
A1  - Dugan, Shannon
A1  - Lee, Sandra L.
A1  - Chao, Hsu
A1  - Dinh, Huyen
A1  - Han, Yi
A1  - Doddapaneni, Harshavardhan
A1  - Worley, Kim C.
A1  - Muzny, Donna M.
A1  - Wheeler, David
A1  - Panfilio, Kristen A.
A1  - Jentzsch, Iris M. Vargas
A1  - Jentzsch, IMV
A1  - Vargo, Edward L.
A1  - Booth, Warren
A1  - Friedrich, Markus
A1  - Weirauch, Matthew T.
A1  - Anderson, Michelle A.E.
A1  - Jones, Jeffery W.
A1  - Mittapalli, Omprakash
A1  - Zhao, Chaoyang
A1  - Zhou, Jing-Jiang
A1  - Evans, Jay D.
A1  - Attardo, Geoffrey M.
A1  - Robertson, Hugh M.
A1  - Zdobnov, Evgeny M.
A1  - Ribeiro, Jose M.C.
A1  - Gibbs, Richard A.
A1  - Werren, John H.
A1  - Palli, Subba R.
A1  - Schal, Coby
A1  - Richards, Stephen
T1  - Unique features of a global human ectoparasite identified through sequencing of the bed bug genome
JF  - Nature Communications
N2  - The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host–symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human–bed bug and symbiont–bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite.
KW  - human ectoparasite
KW  - bed bug
KW  - Cimex lectularius
KW  - genome
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-166221
VL  - 7
IS  - 10165
ER  - 
TY  - JOUR
A1  - Bencurova, Elena
A1  - Shityakov, Sergey
A1  - Schaack, Dominik
A1  - Kaltdorf, Martin
A1  - Sarukhanyan, Edita
A1  - Hilgarth, Alexander
A1  - Rath, Christin
A1  - Montenegro, Sergio
A1  - Roth, Günter
A1  - Lopez, Daniel
A1  - Dandekar, Thomas
T1  - Nanocellulose composites as smart devices with chassis, light-directed DNA Storage, engineered electronic properties, and chip integration
JF  - Frontiers in Bioengineering and Biotechnology
N2  - The rapid development of green and sustainable materials opens up new possibilities in the field of applied research. Such materials include nanocellulose composites that can integrate many components into composites and provide a good chassis for smart devices. In our study, we evaluate four approaches for turning a nanocellulose composite into an information storage or processing device: 1) nanocellulose can be a suitable carrier material and protect information stored in DNA. 2) Nucleotide-processing enzymes (polymerase and exonuclease) can be controlled by light after fusing them with light-gating domains; nucleotide substrate specificity can be changed by mutation or pH change (read-in and read-out of the information). 3) Semiconductors and electronic capabilities can be achieved: we show that nanocellulose is rendered electronic by iodine treatment replacing silicon including microstructures. Nanocellulose semiconductor properties are measured, and the resulting potential including single-electron transistors (SET) and their properties are modeled. Electric current can also be transported by DNA through G-quadruplex DNA molecules; these as well as classical silicon semiconductors can easily be integrated into the nanocellulose composite. 4) To elaborate upon miniaturization and integration for a smart nanocellulose chip device, we demonstrate pH-sensitive dyes in nanocellulose, nanopore creation, and kinase micropatterning on bacterial membranes as well as digital PCR micro-wells. Future application potential includes nano-3D printing and fast molecular processors (e.g., SETs) integrated with DNA storage and conventional electronics. This would also lead to environment-friendly nanocellulose chips for information processing as well as smart nanocellulose composites for biomedical applications and nano-factories.
KW  - nanocellulose
KW  - DNA storage
KW  - light-gated proteins
KW  - single-electron transistors
KW  - protein chip
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-283033
SN  - 2296-4185
VL  - 10
ER  - 
TY  - JOUR
A1  - Bencurova, Elena
A1  - Gupta, Shishir K.
A1  - Sarukhanyan, Edita
A1  - Dandekar, Thomas
T1  - Identification of antifungal targets based on computer modeling
JF  - Journal of Fungi
N2  - Aspergillus fumigatus is a saprophytic, cosmopolitan fungus that attacks patients with a weak immune system. A rational solution against fungal infection aims to manipulate fungal metabolism or to block enzymes essential for Aspergillus survival. Here we discuss and compare different bioinformatics approaches to analyze possible targeting strategies on fungal-unique pathways. For instance, phylogenetic analysis reveals fungal targets, while domain analysis allows us to spot minor differences in protein composition between the host and fungi. Moreover, protein networks between host and fungi can be systematically compared by looking at orthologs and exploiting information from host–pathogen interaction databases. Further data—such as knowledge of a three-dimensional structure, gene expression data, or information from calculated metabolic fluxes—refine the search and rapidly put a focus on the best targets for antimycotics. We analyzed several of the best targets for application to structure-based drug design. Finally, we discuss general advantages and limitations in identification of unique fungal pathways and protein targets when applying bioinformatics tools.
KW  - Aspergillus
KW  - metabolic pathways
KW  - computational modelling
KW  - drug design
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-197670
SN  - 2309-608X
VL  - 4
IS  - 3
ER  - 
TY  - JOUR
A1  - Bencurova, Elena
A1  - Akash, Aman
A1  - Dobson, Renwick C.J.
A1  - Dandekar, Thomas
T1  - DNA storage-from natural biology to synthetic biology
JF  - Computational and Structural Biotechnology Journal
N2  - Natural DNA storage allows cellular differentiation, evolution, the growth of our children and controls all our ecosystems. Here, we discuss the fundamental aspects of DNA storage and recent advances in this field, with special emphasis on natural processes and solutions that can be exploited. We point out new ways of efficient DNA and nucleotide storage that are inspired by nature. Within a few years DNA-based information storage may become an attractive and natural complementation to current electronic data storage systems. We discuss rapid and directed access (e.g. DNA elements such as promotors, enhancers), regulatory signals and modulation (e.g. lncRNA) as well as integrated high-density storage and processing modules (e.g. chromosomal territories). There is pragmatic DNA storage for use in biotechnology and human genetics. We examine DNA storage as an approach for synthetic biology (e.g. light-controlled nucleotide processing enzymes). The natural polymers of DNA and RNA offer much for direct storage operations (read-in, read-out, access control). The inbuilt parallelism (many molecules at many places working at the same time) is important for fast processing of information. Using biology concepts from chromosomal storage, nucleic acid processing as well as polymer material sciences such as electronical effects in enzymes, graphene, nanocellulose up to DNA macramé , DNA wires and DNA-based aptamer field effect transistors will open up new applications gradually replacing classical information storage methods in ever more areas over time (decades).
KW  - DNA
KW  - RNA
KW  - data storage
KW  - natural processing
KW  - synthetic biology
Y1  - 2023
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-349971
SN  - 2001-0370
VL  - 21
ER  - 
TY  - JOUR
A1  - Benavente, Ricardo
A1  - Schmidt-Zachmann, Marion S.
A1  - Hügle-Dörr, B.
A1  - Reimer, G.
A1  - Rose, K. M.
A1  - Scheer, Ulrich
T1  - Identification and definition of nucleolus-related fibrillar bodies in micronucleated cells
N2  - Small nucleolus-related bodies which occur in the nUcleoplasm of " micronuclei" lacking nucleolar organizers have been studied by immunofluorescence microscopy. These bodies stained specifically with three different antibodies directed against proteins that are normally associated with the dense fibrillar component of functional nucleoli, but not with antibodies specific for certain proteins of the granular component or the fibrillar centers. Our data show that, in the absence of rRNA genes, the various constituent proteins characteristic of the dense fibrillar component spontaneously assemble into spherical entities but that the subsequent fusion of these bodies into larger structures is prevented in these micronuclei. The similarity between these nucleolus-related bodies of micronuclei and the prenucleolar bodies characteristic of early stages of nucleologenesis during mitotic telophase is discussed.
Y1  - 1988
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-39423
ER  - 
TY  - JOUR
A1  - Benavente, Ricardo
A1  - Scheer, Ulrich
A1  - Chaly, Nathalie
T1  - Nucleocytoplasmic sorting of macromolecules following mitosis: fate of nuclear constituents after inhibition of pore complex function
N2  - PtK2 cells in which pore complex-mediated transport is blocked by microinjection early in mitosis of a monoclonal antibody (specific for an Mr 68000 pore complex glycoprotein) or of wheat germ agglutinin (WGA) complete cytokinesis. However, their nuclei remain stably arrested in a telophase-like organization characterized by highly condensed chromatin and the absence of nucleoli, indicating a requirement for pore-mediated transport for the reassembly of interphase nuclei. We have now examined this requirement more closely by monitoring the behavior of individual nuclear macromolecules in microinjected cells using immunofluorescence microscopy and have investigated the effect of microinjecting the antibody or WGA on cellular ultrastructure. The absence of nuclear transport did not affect the sequestration into daughter nuclei of components such as DNA, DNA topoisomerase I and the nucleolar protein fibrillarin that are carried through mitosis on chromosomes. On the other hand, lamins, snRNAs and the p68 pore complex glycoprotein, all cytoplasmic during mitosis, remained largely cytoplasmic in the telophase-arrested cells. Electron microscopy showed the nuclei to be surrounded by a doublelayered membrane with some inserted pore complexes. In addition, however, a variety of membranous structures with associated pore complexes was regularly noted in the cytoplasm, suggesting that chromatin may not be essential for the postmitotic formation of pore complexes. We propose that cellular compartmentalization at telophase is a two-step process. First, a nuclear envelope tightly encloses the condensed chromosomes, excluding non-selectively all macromolecules not associated with the chromosomes. Interphase nuclear organization is then progressively restored by selective pore complex-mediated uptake of nuclear proteins from the cytoplasm.
KW  - Cytologie
KW  - Nucleocytoplasmic transport
KW  - nuclear organization
KW  - nuclear envelope
KW  - nucleologenesis
KW  - mitosis
Y1  - 1989
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-40777
ER  - 
TY  - JOUR
A1  - Benavente, Ricardo
A1  - Rose, Kathleen M.
A1  - Reimer, Georg
A1  - Hügle-Dörr, Barbara
A1  - Scheer, Ulrich
T1  - Inhibition of nucleolar reformation after microinjection of antibodies to RNA polymerase I into mitotic cells
N2  - The formation of daughter nuclei and the reformation of nucleolar structures was studied after microinjection of antibodies to RNA polymerase I into dividing cultured cells (PtK2). The fate of several nucleolar proteins representing the three main structural subcomponents of the nucleolus was examined by immunofluorescence and electron microscopy. The results show that the RNA polymerase I antibodies do not interfere with normal mitotic progression or the early steps of nucleologenesis, i.e. , the aggregation of nucleolar material into prenucleolar bodies. However,they inhibit the telophasic coalescence of the prenucleolar bodies into the chromosomal nucleolar organizer regions, thus preventing the formation of new nucleoli. These prenucleolar bodies show a fibrillar organization that also compositionally resembles the dense fibrillar component of interphase nucleoli . We conclude that during normal nucleologenesis the dense fibrillar component forms from preformed entities around nucleolar organizer regions, and that this association seems to be dependent on the presence of an active form of RNA polymerase I.
Y1  - 1987
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-33247
ER  - 
TY  - JOUR
A1  - Benavente, Ricardo
A1  - Reimer, Georg
A1  - Rose, Kathleen M.
A1  - Hügle-Dörr, Barbara
A1  - Scheer, Ulrich
T1  - Nucleolar changes after microinjection of antibodies to RNA polymerase I into the nucleus of mammalian cells
N2  - After microinjection of antibodies against RNA polymerase I into the nuclei of cultured rat kangaroo (PtKz) and rat (RVF-SMC) cells alterations in nucleolar structure and composition were observed. These were detected by electron microscopy and double-label immunofluorescence microscopy using antibodies to proteins representative of the three major components of the nucleolus. The microinjected antibodies produced a progressive loss of the material of the dense fibrillar component (DFC) from the nucleoli which, at 4 h after injection, were transformed into bodies with purely granular component (GC) structure with attached fibrillar centers (FCs). Concomitantly, numerous extranucleolar aggregates appeared in the nucleoplasm which morphologically resembled fragments of the DFC and contained a protein (fibrillarin) diagnostic for this nucleolar structure. These observations indicate that the topological distribution of the material constituting the DFC can be experimentally influenced in interphase cells, apparently by modulating the transcriptional activity of the rRNA genes. These effects are different from nucleolar lesions induced by inhibitory drugs such as actinomycin D-dependent "nucleolar segregation". The structural alterations induced by antibodies to RNA polymerase I resemble, however, the initial events of nucleolar disintegration during mitotic prophase.
Y1  - 1988
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-40666
ER  - 
TY  - JOUR
A1  - Benavente, Ricardo
A1  - Dabauvalle, Marie-Christine
A1  - Scheer, Ulrich
A1  - Chaly, Nathalie
T1  - Functional role of newly formed pore complexes in postmitotic nuclear reorganization
N2  - Many nuclear proteins are released into the cytoplasm at prometaphase and are transported back into the daughter nuclei at the end of mitosis. To determine the role of this reentry in nuclear remodelling during early interphase, we experimentally manipulated nuclear protein uptake in dividing cells. Recently we and others have shown that signal-dependent, pore complex-mediated uptake of nuclear protein is blocked in living cells on microinjection of the lectin wheat germ agglutinin (WGA), or of antibodies such as PI1 that are directed against WGA-binding pore complex glycoproteins. In the present study, we microinjected mitotic PtKz cells with WGA or antibody PIt and followed nuclear reorganization of the daughter cells by immunofluorescence and electron microscopy. The inhibitory effect on nuclear protein uptake was monitored by co-injection of the karyophilic protein nucleoplasmin. When injected by itself early in mitosis, nucleoplasmin became sequestered into the daughter nuclei as they entered telophase. In contrast, nucleoplasmin was excluded from the daughter nuclei in the presence of WGA or antibody PI1 . Although PtKz cells with blocked nuclear protein uptake completed cytokinesis, their nuclei showed a telophaselike organization characterized by highly condensed chromatin surrounded by a nuclear envelope containing a few pore complexes. These findings suggest that pore complexes become functional as early as telophase, in close coincidence with nuclear envelope reformation. They further indicate that the extensive structural rearrangement of the nucleus during the telophase-G1 transition is dependent on the influx of karyophilic proteins from the cytoplasm through the pore complexes, and is not due solely to chromosome- associated components.
Y1  - 1989
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-40754
ER  - 
TY  - JOUR
A1  - Bemm, Felix
A1  - Becker, Dirk
A1  - Larisch, Christina
A1  - Kreuzer, Ines
A1  - Escalante-Perez, Maria
A1  - Schulze, Waltraud X.
A1  - Ankenbrand, Markus
A1  - Van de Weyer, Anna-Lena
A1  - Krol, Elzbieta
A1  - Al-Rasheid, Khaled A.
A1  - Mithöfer, Axel
A1  - Weber, Andreas P.
A1  - Schultz, Jörg
A1  - Hedrich, Rainer
T1  - Venus flytrap carnivorous lifestyle builds on herbivore defense strategies
JF  - Genome Research
N2  - Although the concept of botanical carnivory has been known since Darwin's time, the molecular mechanisms that allow animal feeding remain unknown, primarily due to a complete lack of genomic information. Here, we show that the transcriptomic landscape of the Dionaea trap is dramatically shifted toward signal transduction and nutrient transport upon insect feeding, with touch hormone signaling and protein secretion prevailing. At the same time, a massive induction of general defense responses is accompanied by the repression of cell death-related genes/processes. We hypothesize that the carnivory syndrome of Dionaea evolved by exaptation of ancient defense pathways, replacing cell death with nutrient acquisition.
KW  - Dionaea-muscipula ellis
KW  - Plant utricularia-gibba
KW  - Programmed cell-death
KW  - Genomics data sets
KW  - RNA-SEQ data
KW  - Arabidopsis-thaliana
KW  - Jasmonate perception
KW  - Action potentials
KW  - Stress responses
KW  - Wonderful plants
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-188799
VL  - 26
IS  - 6
ER  - 
TY  - JOUR
A1  - Bell, Peter
A1  - Dabauvalle, Marie-Christine
A1  - Scheer, Ulrich
T1  - In vitro assembly of prenucleolar bodies in Xenopus egg extract
N2  - Nuclei assembled in Xenopus egg extract from purified DNA or chromatin resemble their natural counterparts in a number of structural and functional features. However, the most obvious structural element of normal interphase nuclei, the nucleolus, is absent from the in vitro reconstituted nuclei. By EM, cytological silver staining, and immunofluorescence microscopy employing antibodies directed against various nucleolar components we show that nuclei assembled in vitro contain numerous distinct aggregates that resemble prenucleolar bodies (PNBs) by several criteria. Formation of these PNB-like structures requires pore complex-mediated nuclear transport of proteins but is independent of the genetic content of the in vitro nuclei as well as transcriptional and translational events. Our data indicate that nuclei assembled in vitro are capable of initiating early steps of nucleologenesis but that the resulting PNBs are unable to fuse with each other, probably due to the absence of a functional nucleolus organizer. With appropriate modifications, this experimental system should be useful to define and analyze conditions promoting the site-specific assembly of PNBs into a coherent nucleolar body.
Y1  - 1992
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-34233
ER  - 
TY  - JOUR
A1  - Beisser, Daniela
A1  - Grohme, Markus A.
A1  - Kopka, Joachim
A1  - Frohme, Marcus
A1  - Schill, Ralph O.
A1  - Hengherr, Steffen
A1  - Dandekar, Thomas
A1  - Klau, Gunnar W.
A1  - Dittrich, Marcus
A1  - Müller, Tobias
T1  - Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum
N2  - Background: Tardigrades are multicellular organisms, resistant to extreme environmental changes such as heat, drought, radiation and freezing. They outlast these conditions in an inactive form (tun) to escape damage to cellular structures and cell death. Tardigrades are apparently able to prevent or repair such damage and are therefore a crucial model organism for stress tolerance. Cultures of the tardigrade Milnesium tardigradum were dehydrated by removing the surrounding water to induce tun formation. During this process and the subsequent rehydration, metabolites were measured in a time series by GC-MS. Additionally expressed sequence tags are available, especially libraries generated from the active and inactive state. The aim of this integrated analysis is to trace changes in tardigrade metabolism and identify pathways responsible for their extreme resistance against physical stress. Results: In this study we propose a novel integrative approach for the analysis of metabolic networks to identify modules of joint shifts on the transcriptomic and metabolic levels. We derive a tardigrade-specific metabolic network represented as an undirected graph with 3,658 nodes (metabolites) and 4,378 edges (reactions). Time course metabolite profiles are used to score the network nodes showing a significant change over time. The edges are scored according to information on enzymes from the EST data. Using this combined information, we identify a key subnetwork (functional module) of concerted changes in metabolic pathways, specific for de- and rehydration. The module is enriched in reactions showing significant changes in metabolite levels and enzyme abundance during the transition. It resembles the cessation of a measurablemetabolism (e.g. glycolysis and amino acid anabolism) during the tun formation, the production of storage metabolites and bioprotectants, such as DNA stabilizers, and the generation of amino acids and cellular components from monosaccharides as carbon and energy source during rehydration. Conclusions: The functional module identifies relationships among changed metabolites (e.g. spermidine) and reactions and provides first insights into important altered metabolic pathways. With sparse and diverse data available, the presented integrated metabolite network approach is suitable to integrate all existing data and analyse it in a combined manner.
KW  - Milnesium tardigradum
KW  - Integrated network analysis
KW  - Functional modules
KW  - Metabolic profiles
KW  - Metabolic pathways
KW  - Trend test
Y1  - 2012
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-75241
ER  - 
TY  - JOUR
A1  - Beier, Hildburg
A1  - Gätschenberger, Heike
A1  - Azzami, Klara
A1  - Tautz, Jürgen
T1  - Antibacterial Immune Competence of Honey Bees (Apis mellifera) Is Adapted to Different Life Stages and Environmental Risks
JF  - PLoS ONE
N2  - The development of all honey bee castes proceeds through three different life stages all of which encounter microbial infections to a various extent. We have examined the immune strength of honey bees across all developmental stages with emphasis on the temporal expression of cellular and humoral immune responses upon artificial challenge with viable Escherichia coli bacteria. We employed a broad array of methods to investigate defence strategies of infected individuals: (a) fate of bacteria in the haemocoel; (b) nodule formation and (c) induction of antimicrobial peptides (AMPs). Newly emerged adult worker bees and drones were able to activate efficiently all examined immune reactions. The number of viable bacteria circulating in the haemocoel of infected bees declined rapidly by more than two orders of magnitude within the first 4–6 h post-injection (p.i.), coinciding with the occurrence of melanised nodules. Antimicrobial activity, on the other hand, became detectable only after the initial bacterial clearance. These two temporal patterns of defence reactions very likely represent the constitutive cellular and the induced humoral immune response. A unique feature of honey bees is that a fraction of worker bees survives the winter season in a cluster mostly engaged in thermoregulation. We show here that the overall immune strength of winter bees matches that of young summer bees although nodulation reactions are not initiated at all. As expected, high doses of injected viable E.coli bacteria caused no mortality in larvae or adults of each age. However, drone and worker pupae succumbed to challenge with E.coli even at low doses, accompanied by a premature darkening of the pupal body. In contrast to larvae and adults, we observed no fast clearance of viable bacteria and no induction of AMPs but a rapid proliferation of E.coli bacteria in the haemocoel of bee pupae ultimately leading to their death.
KW  - escherichia coli infections
KW  - honey bees
KW  - bees
KW  - antimicrobials
KW  - bacterial pathogens
KW  - larvae
KW  - pupae
KW  - winter
Y1  - 2013
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-96895
ER  - 
TY  - JOUR
A1  - Beetz, M. Jerome
A1  - Kraus, Christian
A1  - el Jundi, Basil
T1  - Neural representation of goal direction in the monarch butterfly brain
JF  - Nature Communications
N2  - Neural processing of a desired moving direction requires the continuous comparison between the current heading and the goal direction. While the neural basis underlying the current heading is well-studied, the coding of the goal direction remains unclear in insects. Here, we used tetrode recordings in tethered flying monarch butterflies to unravel how a goal direction is represented in the insect brain. While recording, the butterflies maintained robust goal directions relative to a virtual sun. By resetting their goal directions, we found neurons whose spatial tuning was tightly linked to the goal directions. Importantly, their tuning was unaffected when the butterflies changed their heading after compass perturbations, showing that these neurons specifically encode the goal direction. Overall, we here discovered invertebrate goal-direction neurons that share functional similarities to goal-direction cells reported in mammals. Our results give insights into the evolutionarily conserved principles of goal-directed spatial orientation in animals.
KW  - animal behaviour
KW  - navigation
KW  - neuroscience
Y1  - 2023
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-358073
VL  - 14
ER  - 
TY  - JOUR
A1  - Beetz, M. Jerome
A1  - Hechavarría, Julio C.
T1  - Neural processing of naturalistic echolocation signals in bats
JF  - Frontiers in Neural Circuits
N2  - Echolocation behavior, a navigation strategy based on acoustic signals, allows scientists to explore neural processing of behaviorally relevant stimuli. For the purpose of orientation, bats broadcast echolocation calls and extract spatial information from the echoes. Because bats control call emission and thus the availability of spatial information, the behavioral relevance of these signals is undiscussable. While most neurophysiological studies, conducted in the past, used synthesized acoustic stimuli that mimic portions of the echolocation signals, recent progress has been made to understand how naturalistic echolocation signals are encoded in the bat brain. Here, we review how does stimulus history affect neural processing, how spatial information from multiple objects and how echolocation signals embedded in a naturalistic, noisy environment are processed in the bat brain. We end our review by discussing the huge potential that state-of-the-art recording techniques provide to gain a more complete picture on the neuroethology of echolocation behavior.
KW  - biosonar
KW  - neural coding
KW  - naturalistic stimuli
KW  - bats
KW  - acoustic stream
KW  - neuroethology
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-274605
SN  - 1662-5110
VL  - 16
ER  - 
TY  - JOUR
A1  - Beer, Katharina
A1  - Steffan-Dewenter, Ingolf
A1  - Härtel, Stephan
A1  - Helfrich-Förster, Charlotte
T1  - A new device for monitoring individual activity rhythms of honey bees reveals critical effects of the social environment on behavior
JF  - Journal of Comparative Physiology A
N2  - Chronobiological studies of individual activity rhythms in social insects can be constrained by the artificial isolation of individuals from their social context. We present a new experimental set-up that simultaneously measures the temperature rhythm in a queen-less but brood raising mini colony and the walking activity rhythms of singly kept honey bees that have indirect social contact with it. Our approach enables monitoring of individual bees in the social context of a mini colony under controlled laboratory conditions. In a pilot experiment, we show that social contact with the mini colony improves the survival of monitored young individuals and affects locomotor activity patterns of young and old bees. When exposed to conflicting Zeitgebers consisting of a light-dark (LD) cycle that is phase-delayed with respect to the mini colony rhythm, rhythms of young and old bees are socially synchronized with the mini colony rhythm, whereas isolated bees synchronize to the LD cycle. We conclude that the social environment is a stronger Zeitgeber than the LD cycle and that our new experimental set-up is well suited for studying the mechanisms of social entrainment in honey bees.
KW  - Social entrainment
KW  - Foragers
KW  - Nurses
KW  - Locomotor activity
KW  - Temperature rhythms
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-188030
VL  - 202
IS  - 8
ER  - 
TY  - JOUR
A1  - Beer, Katharina
A1  - Schenk, Mariela
A1  - Helfrich-Förster, Charlotte
A1  - Holzschuh, Andrea
T1  - The circadian clock uses different environmental time cues to synchronize emergence and locomotion of the solitary bee Osmia bicornis
JF  - Scientific Reports
N2  - Life on earth adapted to the daily reoccurring changes in environment by evolving an endogenous circadian clock. Although the circadian clock has a crucial impact on survival and behavior of solitary bees, many aspects of solitary bee clock mechanisms remain unknown. Our study is the first to show that the circadian clock governs emergence in Osmia bicornis, a bee species which overwinters as adult inside its cocoon. Therefore, its eclosion from the pupal case is separated by an interjacent diapause from its emergence in spring. We show that this bee species synchronizes its emergence to the morning. The daily rhythms of emergence are triggered by temperature cycles but not by light cycles. In contrast to this, the bee’s daily rhythms in locomotion are synchronized by light cycles. Thus, we show that the circadian clock of O. bicornis is set by either temperature or light, depending on what activity is timed. Light is a valuable cue for setting the circadian clock when bees have left the nest. However, for pre-emerged bees, temperature is the most important cue, which may represent an evolutionary adaptation of the circadian system to the cavity-nesting life style of O. bicornis.
KW  - Behavioural ecology
KW  - Evolutionary developmental biology
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-202721
VL  - 9
ER  - 
TY  - JOUR
A1  - Beer, Katharina
A1  - Joschinski, Jens
A1  - Sastre, Alazne Arrazola
A1  - Krauss, Jochen
A1  - Helfrich-Förster, Charlotte
T1  - A damping circadian clock drives weak oscillations in metabolism and locomotor activity of aphids (Acyrthosiphon pisum)
JF  - Scientific Reports
N2  - Timing seasonal events, like reproduction or diapause, is crucial for the survival of many species. Global change causes phenologies worldwide to shift, which requires a mechanistic explanation of seasonal time measurement. Day length (photoperiod) is a reliable indicator of winter arrival, but it remains unclear how exactly species measure day length. A reference for time of day could be provided by a circadian clock, by an hourglass clock, or, as some newer models suggest, by a damped circadian clock. However, damping of clock outputs has so far been rarely observed. To study putative clock outputs of Acyrthosiphon pisum aphids, we raised individual nymphs on coloured artificial diet, and measured rhythms in metabolic activity in light-dark illumination cycles of 16:08 hours (LD) and constant conditions (DD). In addition, we kept individuals in a novel monitoring setup and measured locomotor activity. We found that A. pisum is day-active in LD, potentially with a bimodal distribution. In constant darkness rhythmicity of locomotor behaviour persisted in some individuals, but patterns were mostly complex with several predominant periods. Metabolic activity, on the other hand, damped quickly. A damped circadian clock, potentially driven by multiple oscillator populations, is the most likely explanation of our results.
KW  - circadian mechanisms
KW  - behavioural ecology
KW  - damped circadian clock
KW  - Acyrthosiphon pisum
Y1  - 2017
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-170020
VL  - 7
IS  - 14906
ER  - 
TY  - JOUR
A1  - Beer, Katharina
A1  - Härtel, Stephan
A1  - Helfrich-Förster, Charlotte
T1  - The pigment-dispersing factor neuronal network systematically grows in developing honey bees
JF  - The Journal of Comparative Neurology
N2  - The neuropeptide pigment-dispersing factor (PDF) plays a prominent role in the circadian clock of many insects including honey bees. In the honey bee brain, PDF is expressed in about 15 clock neurons per hemisphere that lie between the central brain and the optic lobes. As in other insects, the bee PDF neurons form wide arborizations in the brain, but certain differences are evident. For example, they arborize only sparsely in the accessory medulla (AME), which serves as important communication center of the circadian clock in cockroaches and flies. Furthermore, all bee PDF neurons cluster together, which makes it impossible to distinguish individual projections. Here, we investigated the developing bee PDF network and found that the first three PDF neurons arise in the third larval instar and form a dense network of varicose fibers at the base of the developing medulla that strongly resembles the AME of hemimetabolous insects. In addition, they send faint fibers toward the lateral superior protocerebrum. In last larval instar, PDF cells with larger somata appear and send fibers toward the distal medulla and the medial protocerebrum. In the dorsal part of the medulla serpentine layer, a small PDF knot evolves from which PDF fibers extend ventrally. This knot disappears during metamorphosis and the varicose arborizations in the putative AME become fainter. Instead, a new strongly stained PDF fiber hub appears in front of the lobula. Simultaneously, the number of PDF neurons increases and the PDF neuronal network in the brain gets continuously more complex.
KW  - apis mellifera
KW  - circadian clock
KW  - immunohistochemistry
KW  - larval and pupal development
KW  - neuroanatomy
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-257300
VL  - 530
IS  - 9
ER  - 
TY  - JOUR
A1  - Beer, Katharina
A1  - Helfrich-Förster, Charlotte
T1  - Model and Non-model Insects in Chronobiology
JF  - Frontiers in Behavioral Neuroscience
N2  - The fruit fly Drosophila melanogaster is an established model organism in chronobiology, because genetic manipulation and breeding in the laboratory are easy. The circadian clock neuroanatomy in D. melanogaster is one of the best-known clock networks in insects and basic circadian behavior has been characterized in detail in this insect. Another model in chronobiology is the honey bee Apis mellifera, of which diurnal foraging behavior has been described already in the early twentieth century. A. mellifera hallmarks the research on the interplay between the clock and sociality and complex behaviors like sun compass navigation and time-place-learning. Nevertheless, there are aspects of clock structure and function, like for example the role of the clock in photoperiodism and diapause, which can be only insufficiently investigated in these two models. Unlike high-latitude flies such as Chymomyza costata or D. ezoana, cosmopolitan D. melanogaster flies do not display a photoperiodic diapause. Similarly, A. mellifera bees do not go into “real” diapause, but most solitary bee species exhibit an obligatory diapause. Furthermore, sociality evolved in different Hymenoptera independently, wherefore it might be misleading to study the social clock only in one social insect. Consequently, additional research on non-model insects is required to understand the circadian clock in Diptera and Hymenoptera. In this review, we introduce the two chronobiology model insects D. melanogaster and A. mellifera, compare them with other insects and show their advantages and limitations as general models for insect circadian clocks.
KW  - circadian clock
KW  - complex behavior
KW  - diapause
KW  - sociality
KW  - Drosophila melanogaster
KW  - Apis mellifera
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-218721
SN  - 1662-5153
VL  - 14
ER  - 
TY  - JOUR
A1  - Beer, Katharina
A1  - Helfrich-Förster, Charlotte
T1  - Post-embryonic Development of the Circadian Clock Seems to Correlate With Social Life Style in Bees
JF  - Frontiers in Cell and Developmental Biology
N2  - Social life style can influence many aspects of an animal’s daily life, but it has not yet been clarified, whether development of the circadian clock in social and solitary living bees differs. In a comparative study, with the social honey bee, Apis mellifera, and the solitary mason bee, Osmia bicornis, we now found indications for a differentially timed clock development in social and solitary bees. Newly emerged solitary bees showed rhythmic locomotion right away and the number of neurons in the brain that produce the clock component pigment-dispersing factor (PDF) did not change during aging of the adult solitary bee. Honey bees on the other hand, showed no circadian locomotion directly after emergence and the neuronal clock network continued to grow after emergence. Social bees appear to emerge at an early developmental stage at which the circadian clock is still immature, but bees are already able to fulfill in-hive tasks.
KW  - social
KW  - honey bee
KW  - solitary bee
KW  - circadian clock
KW  - activity rhythm
KW  - neuronal network
KW  - development
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-216450
SN  - 2296-634X
VL  - 8
ER  - 
TY  - JOUR
A1  - Becker, Nils
A1  - Kucharski, Robert
A1  - Rössler, Wolfgang
A1  - Maleszka, Ryszard
T1  - Age‐dependent transcriptional and epigenomic responses to light exposure in the honey bee brain
JF  - FEBS Open Bio
N2  - Light is a powerful environmental stimulus of special importance in social honey bees that undergo a behavioral transition from in-hive to outdoor foraging duties. Our previous work has shown that light exposure induces structural neuronal plasticity in the mushroom bodies (MBs), a brain center implicated in processing inputs from sensory modalities. Here, we extended these analyses to the molecular level to unravel light-induced transcriptomic and epigenomic changes in the honey bee brain. We have compared gene expression in brain compartments of 1- and 7-day-old light-exposed honey bees with age-matched dark-kept individuals. We have found a number of differentially expressed genes (DEGs), both novel and conserved, including several genes with reported roles in neuronal plasticity. Most of the DEGs show age-related changes in the amplitude of light-induced expression and are likely to be both developmentally and environmentally regulated. Some of the DEGs are either known to be methylated or are implicated in epigenetic processes suggesting that responses to light exposure are at least partly regulated at the epigenome level. Consistent with this idea light alters the DNA methylation pattern of bgm, one of the DEGs affected by light exposure, and the expression of microRNA miR-932. This confirms the usefulness of our approach to identify candidate genes for neuronal plasticity and provides evidence for the role of epigenetic processes in driving the molecular responses to visual stimulation.
KW  - DNA methylation
KW  - insect brain
KW  - light-induced gene expression
KW  - microRNA
KW  - neuronal plasticity
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-147080
VL  - 6
IS  - 7
ER  - 
TY  - JOUR
A1  - Beck, Sebastian
A1  - Yu-Strzelczyk, Jing
A1  - Pauls, Dennis
A1  - Constantin, Oana M.
A1  - Gee, Christine E.
A1  - Ehmann, Nadine
A1  - Kittel, Robert J.
A1  - Nagel, Georg
A1  - Gao, Shiqiang
T1  - Synthetic light-activated ion channels for optogenetic activation and inhibition
JF  - Frontiers in Neuroscience
N2  - Optogenetic manipulation of cells or living organisms became widely used in neuroscience following the introduction of the light-gated ion channel channelrhodopsin-2 (ChR2). ChR2 is a non-selective cation channel, ideally suited to depolarize and evoke action potentials in neurons. However, its calcium (Ca2\(^{2+}\)) permeability and single channel conductance are low and for some applications longer-lasting increases in intracellular Ca\(^{2+}\) might be desirable. Moreover, there is need for an efficient light-gated potassium (K\(^{+}\)) channel that can rapidly inhibit spiking in targeted neurons. Considering the importance of Ca\(^{2+}\) and K\(^{+}\) in cell physiology, light-activated Ca\(^{2+}\)-permeant and K\(^{+}\)-specific channels would be welcome additions to the optogenetic toolbox. Here we describe the engineering of novel light-gated Ca\(^{2+}\)-permeant and K\(^{+}\)-specific channels by fusing a bacterial photoactivated adenylyl cyclase to cyclic nucleotide-gated channels with high permeability for Ca\(^{2+}\) or for K\(^{+}\), respectively. Optimized fusion constructs showed strong light-gated conductance in Xenopus laevis oocytes and in rat hippocampal neurons. These constructs could also be used to control the motility of Drosophila melanogaster larvae, when expressed in motoneurons. Illumination led to body contraction when motoneurons expressed the light-sensitive Ca\(^{2+}\)-permeant channel, and to body extension when expressing the light-sensitive K\(^{+}\) channel, both effectively and reversibly paralyzing the larvae. Further optimization of these constructs will be required for application in adult flies since both constructs led to eclosion failure when expressed in motoneurons.
KW  - optogenetics
KW  - calcium
KW  - potassium
KW  - bPAC
KW  - CNG channel
KW  - cAMP
KW  - Drosophila melanogaster motoneuron
KW  - rat hippocampal neurons
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-177520
VL  - 12
IS  - 643
ER  - 
TY  - JOUR
A1  - Beck, Katherina
A1  - Hovhanyan, Anna
A1  - Menegazzi, Pamela
A1  - Helfrich-Förster, Charlotte
A1  - Raabe, Thomas
T1  - Drosophila RSK Influences the Pace of the Circadian Clock by Negative Regulation of Protein Kinase Shaggy Activity
JF  - Frontiers in Molecular Neuroscience
N2  - Endogenous molecular circadian clocks drive daily rhythmic changes at the cellular, physiological, and behavioral level for adaptation to and anticipation of environmental signals. The core molecular system consists of autoregulatory feedback loops, where clock proteins inhibit their own transcription. A complex and not fully understood interplay of regulatory proteins influences activity, localization and stability of clock proteins to set the pace of the clock. This study focuses on the molecular function of Ribosomal S6 Kinase (RSK) in the Drosophila melanogaster circadian clock. Mutations in the human rsk2 gene cause Coffin–Lowry syndrome, which is associated with severe mental disabilities. Knock-out studies with Drosophila ortholog rsk uncovered functions in synaptic processes, axonal transport and adult behavior including associative learning and circadian activity. However, the molecular targets of RSK remain elusive. Our experiments provide evidence that RSK acts in the key pace maker neurons as a negative regulator of Shaggy (SGG) kinase activity, which in turn determines timely nuclear entry of the clock proteins Period and Timeless to close the negative feedback loop. Phosphorylation of serine 9 in SGG is mediated by the C-terminal kinase domain of RSK, which is in agreement with previous genetic studies of RSK in the circadian clock but argues against the prevailing view that only the N-terminal kinase domain of RSK proteins carries the effector function. Our data provide a mechanistic explanation how RSK influences the molecular clock and imply SGG S9 phosphorylation by RSK and other kinases as a convergence point for diverse cellular and external stimuli.
KW  - circadian clock
KW  - Period
KW  - Timeless
KW  - Shaggy kinase
KW  - RSK
KW  - Coffin–Lowry syndrome
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-196034
SN  - 1662-5099
VL  - 11
IS  - 122
ER  - 
TY  - JOUR
A1  - Becher, Isabelle
A1  - Andrés-Pons, Amparo
A1  - Romanov, Natalie
A1  - Stein, Frank
A1  - Schramm, Maike
A1  - Baudin, Florence
A1  - Helm, Dominic
A1  - Kurzawa, Nils
A1  - Mateus, André
A1  - Mackmull, Marie-Therese
A1  - Typas, Athanasios
A1  - Müller, Christoph W.
A1  - Bork, Peer
A1  - Beck, Martin
A1  - Savitski, Mikhail M.
T1  - Pervasive Protein Thermal Stability Variation during the Cell Cycle
JF  - Cell
N2  - Quantitative mass spectrometry has established proteome-wide regulation of protein abundance and post-translational modifications in various biological processes. Here, we used quantitative mass spectrometry to systematically analyze the thermal stability and solubility of proteins on a proteome-wide scale during the eukaryotic cell cycle. We demonstrate pervasive variation of these biophysical parameters with most changes occurring in mitosis and G1. Various cellular pathways and components vary in thermal stability, such as cell-cycle factors, polymerases, and chromatin remodelers. We demonstrate that protein thermal stability serves as a proxy for enzyme activity, DNA binding, and complex formation in situ. Strikingly, a large cohort of intrinsically disordered and mitotically phosphorylated proteins is stabilized and solubilized in mitosis, suggesting a fundamental remodeling of the biophysical environment of the mitotic cell. Our data represent a rich resource for cell, structural, and systems biologists interested in proteome regulation during biological transitions.
KW  - thermal proteome profiling
KW  - cell cycle
KW  - proteomics
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-221565
VL  - 173
ER  - 
TY  - JOUR
A1  - Becam, Jérôme
A1  - Walter, Tim
A1  - Burgert, Anne
A1  - Schlegel, Jan
A1  - Sauer, Markus
A1  - Seibel, Jürgen
A1  - Schubert-Unkmeir, Alexandra
T1  - Antibacterial activity of ceramide and ceramide analogs against pathogenic Neisseria
JF  - Scientific Reports
N2  - Certain fatty acids and sphingoid bases found at mucosal surfaces are known to have antibacterial activity and are thought to play a more direct role in innate immunity against bacterial infections. Herein, we analysed the antibacterial activity of sphingolipids, including the sphingoid base sphingosine as well as short-chain C\(_{6}\) and long-chain C\(_{16}\)-ceramides and azido-functionalized ceramide analogs against pathogenic Neisseriae. Determination of the minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) demonstrated that short-chain ceramides and a ω-azido-functionalized C\(_{6}\)-ceramide were active against Neisseria meningitidis and N. gonorrhoeae, whereas they were inactive against Escherichia coli and Staphylococcus aureus. Kinetic assays showed that killing of N. meningitidis occurred within 2 h with ω–azido-C\(_{6}\)-ceramide at 1 X the MIC. Of note, at a bactericidal concentration, ω–azido-C\(_{6}\)-ceramide had no significant toxic effect on host cells. Moreover, lipid uptake and localization was studied by flow cytometry and confocal laser scanning microscopy (CLSM) and revealed a rapid uptake by bacteria within 5 min. CLSM and super-resolution fluorescence imaging by direct stochastic optical reconstruction microscopy demonstrated homogeneous distribution of ceramide analogs in the bacterial membrane. Taken together, these data demonstrate the potent bactericidal activity of sphingosine and synthetic short-chain ceramide analogs against pathogenic Neisseriae.
KW  - ceramide analogs
KW  - Neisseria
KW  - ceramide
Y1  - 2017
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-159367
VL  - 7
ER  - 
TY  - JOUR
A1  - Bazihizina, Nadia
A1  - Böhm, Jennifer
A1  - Messerer, Maxim
A1  - Stigloher, Christian
A1  - Müller, Heike M.
A1  - Cuin, Tracey Ann
A1  - Maierhofer, Tobias
A1  - Cabot, Joan
A1  - Mayer, Klaus F. X.
A1  - Fella, Christian
A1  - Huang, Shouguang
A1  - Al‐Rasheid, Khaled A. S.
A1  - Alquraishi, Saleh
A1  - Breadmore, Michael
A1  - Mancuso, Stefano
A1  - Shabala, Sergey
A1  - Ache, Peter
A1  - Zhang, Heng
A1  - Zhu, Jian‐Kang
A1  - Hedrich, Rainer
A1  - Scherzer, Sönke
T1  - Stalk cell polar ion transport provide for bladder‐based salinity tolerance in Chenopodium quinoa
JF  - New Phytologist
N2  - Chenopodium quinoa uses epidermal bladder cells (EBCs) to sequester excess salt. Each EBC complex consists of a leaf epidermal cell, a stalk cell, and the bladder.

Under salt stress, sodium (Na\(^{+}\)), chloride (Cl\(^{−}\)), potassium (K\(^{+}\)) and various metabolites are shuttled from the leaf lamina to the bladders. Stalk cells operate as both a selectivity filter and a flux controller.

In line with the nature of a transfer cell, advanced transmission electron tomography, electrophysiology, and fluorescent tracer flux studies revealed the stalk cell’s polar organization and bladder‐directed solute flow.

RNA sequencing and cluster analysis revealed the gene expression profiles of the stalk cells. Among the stalk cell enriched genes, ion channels and carriers as well as sugar transporters were most pronounced. Based on their electrophysiological fingerprint and thermodynamic considerations, a model for stalk cell transcellular transport was derived.
KW  - halophyte
KW  - polar ion transport
KW  - quinoa
KW  - salt tolerance
KW  - stalk cell
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-287222
VL  - 235
IS  - 5
SP  - 1822
EP  - 1835
ER  - 
TY  - JOUR
A1  - Baur, Stefanie
A1  - Rautenberg, Maren
A1  - Faulstich, Manuela
A1  - Grau, Timo
A1  - Severin, Yannik
A1  - Unger, Clemens
A1  - Hoffmann, Wolfgang H.
A1  - Rudel, Thomas
A1  - Autenrieth, Ingo B.
A1  - Weidenmaier, Christopher
T1  - A Nasal Epithelial Receptor for Staphylococcus aureus WTA Governs Adhesion to Epithelial Cells and Modulates Nasal Colonization
JF  - PLOS PATHOGENS
N2  - Nasal colonization is a major risk factor for S. aureus infections. The mechanisms responsible for colonization are still not well understood and involve several factors on the host and the bacterial side. One key factor is the cell wall teichoic acid (WTA) of S. aureus, which governs direct interactions with nasal epithelial surfaces. We report here the first receptor for the cell wall glycopolymer WTA on nasal epithelial cells. In several assay systems this type F-scavenger receptor, termed SREC-I, bound WTA in a charge dependent manner and mediated adhesion to nasal epithelial cells in vitro. The impact of WTA and SREC-I interaction on epithelial adhesion was especially pronounced under shear stress, which resembles the conditions found in the nasal cavity. Most importantly, we demonstrate here a key role of the WTA-receptor interaction in a cotton rat model of nasal colonization. When we inhibited WTA mediated adhesion with a SREC-I antibody, nasal colonization in the animal model was strongly reduced at the early onset of colonization. More importantly, colonization stayed low over an extended period of 6 days. Therefore we propose targeting of this glycopolymer-receptor interaction as a novel strategy to prevent or control S. aureus nasal colonization.
KW  - SREC-I
KW  - clumping factor-B
KW  - scavender receptor
KW  - teichoic acids
KW  - surface proteins
KW  - cotton rats
KW  - carriage
KW  - determinant
KW  - infections
KW  - expression
Y1  - 2014
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-116280
SN  - 1553-7374
VL  - 10
IS  - 5
ER  - 
TY  - JOUR
A1  - Baur, Florentin
A1  - Nietzer, Sarah L.
A1  - Kunz, Meik
A1  - Saal, Fabian
A1  - Jeromin, Julian
A1  - Matschos, Stephanie
A1  - Linnebacher, Michael
A1  - Walles, Heike
A1  - Dandekar, Thomas
A1  - Dandekar, Gudrun
T1  - Connecting cancer pathways to tumor engines: a stratification tool for colorectal cancer combining human in vitro tissue models with boolean in silico models
JF  - Cancers
N2  - To improve and focus preclinical testing, we combine tumor models based on a decellularized tissue matrix with bioinformatics to stratify tumors according to stage-specific mutations that are linked to central cancer pathways. We generated tissue models with BRAF-mutant colorectal cancer (CRC) cells (HROC24 and HROC87) and compared treatment responses to two-dimensional (2D) cultures and xenografts. As the BRAF inhibitor vemurafenib is—in contrast to melanoma—not effective in CRC, we combined it with the EGFR inhibitor gefitinib. In general, our 3D models showed higher chemoresistance and in contrast to 2D a more active HGFR after gefitinib and combination-therapy. In xenograft models murine HGF could not activate the human HGFR, stressing the importance of the human microenvironment. In order to stratify patient groups for targeted treatment options in CRC, an in silico topology with different stages including mutations and changes in common signaling pathways was developed. We applied the established topology for in silico simulations to predict new therapeutic options for BRAF-mutated CRC patients in advanced stages. Our in silico tool connects genome information with a deeper understanding of tumor engines in clinically relevant signaling networks which goes beyond the consideration of single drivers to improve CRC patient stratification.
KW  - in silico simulation
KW  - 3D tissue models
KW  - colorectal cancer
KW  - BRAF mutation
KW  - targeted therapy
KW  - stratification
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-193798
SN  - 2072-6694
VL  - 12
IS  - 1
ER  - 
TY  - JOUR
A1  - Batzke, Katharina
A1  - Büchel, Gabriele
A1  - Hansen, Wiebke
A1  - Schramm, Alexander
T1  - TrkB-target Galectin-1 impairs immune activation and radiation responses in neuroblastoma: implications for tumour therapy
JF  - International Journal of Molecular Sciences
N2  - Galectin-1 (Gal-1) has been described to promote tumour growth by inducing angiogenesis and to contribute to the tumour immune escape. We had previously identified up-regulation of Gal-1 in preclinical models of aggressive neuroblastoma (NB), the most common extracranial tumour of childhood. While Gal-1 did not confer a survival advantage in the absence of exogenous stressors, Gal-1 contributed to enhanced cell migratory and invasive properties. Here, we review these findings and extend them by analyzing Gal-1 mediated effects on immune cell regulation and radiation resistance. In line with previous results, cell autonomous effects as well as paracrine functions contribute to Gal-1 mediated pro-tumourigenic functions. Interfering with Gal-1 functions in vivo will add to a better understanding of the role of the Gal-1 axis in the complex tumour-host interaction during immune-, chemo- and radiotherapy of neuroblastoma.
KW  - Galectin-1
KW  - radiation response
KW  - neuroblastoma
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-285097
SN  - 1422-0067
VL  - 19
IS  - 3
ER  - 
TY  - JOUR
A1  - Batram, Christopher
A1  - Jones, Nivola G.
A1  - Janzen, Christian J.
A1  - Markert, Sebastian M.
A1  - Engstler, Markus
T1  - Expression site attenuation mechanistically links antigenic variation and development in Trypanosoma brucei
JF  - eLife
N2  - We have discovered a new mechanism of monoallelic gene expression that links antigenic variation, cell cycle, and development in the model parasite Trypanosoma brucei. African trypanosomes possess hundreds of variant surface glycoprotein (VSG) genes, but only one is expressed from a telomeric expression site (ES) at any given time. We found that the expression of a second VSG alone is sufficient to silence the active VSG gene and directionally attenuate the ES by disruptor of telomeric silencing-1B (DOT1B)-mediated histone methylation. Three conserved expression-site-associated genes (ESAGs) appear to serve as signal for ES attenuation. Their depletion causes G1-phase dormancy and reversible initiation of the slender-to-stumpy differentiation pathway. ES-attenuated slender bloodstream trypanosomes gain full developmental competence for transformation to the tsetse fly stage. This surprising connection between antigenic variation and developmental progression provides an unexpected point of attack against the deadly sleeping sickness.
KW  - antigenic variation
KW  - expression site attenuation
KW  - developmental reprogramming
KW  - cell biology
KW  - genes and chromosomes
KW  - Trypanosoma brucei
KW  - variant surface glycoprotein (VSG)
KW  - monoallelic expression
Y1  - 2014
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-119727
SN  - 2050-084X
VL  - 3
IS  - e02324
ER  - 
TY  - JOUR
A1  - Basset, Yves
A1  - Cizek, Lukas
A1  - Cuénoud, Philippe
A1  - Didham, Raphael K.
A1  - Novotny, Vojtech
A1  - Ødegaard, Frode
A1  - Roslin, Tomas
A1  - Tishechkin, Alexey K.
A1  - Schmidl, Jürgen
A1  - Winchester, Neville N.
A1  - Roubik, David W.
A1  - Aberlenc, Henri-Pierre
A1  - Bail, Johannes
A1  - Barrios, Hector
A1  - Bridle, Jonathan R.
A1  - Castaño-Meneses, Gabriela
A1  - Corbara, Bruno
A1  - Curletti, Gianfranco
A1  - da Rocha, Wesley Duarte
A1  - De Bakker, Domir
A1  - Delabie, Jacques H. C.
A1  - Dejean, Alain
A1  - Fagan, Laura L.
A1  - Floren, Andreas
A1  - Kitching, Roger L.
A1  - Medianero, Enrique
A1  - de Oliveira, Evandro Gama
A1  - Orivel, Jerome
A1  - Pollet, Marc
A1  - Rapp, Mathieu
A1  - Ribeiro, Servio P.
A1  - Roisin, Yves
A1  - Schmidt, Jesper B.
A1  - Sørensen, Line
A1  - Lewinsohn, Thomas M.
A1  - Leponce, Maurice
T1  - Arthropod Distribution in a Tropical Rainforest: Tackling a Four Dimensional Puzzle
JF  - PLoS ONE
N2  - Quantifying the spatio-temporal distribution of arthropods in tropical rainforests represents a first step towards scrutinizing the global distribution of biodiversity on Earth. To date most studies have focused on narrow taxonomic groups or lack a design that allows partitioning of the components of diversity. Here, we consider an exceptionally large dataset (113,952 individuals representing 5,858 species), obtained from the San Lorenzo forest in Panama, where the phylogenetic breadth of arthropod taxa was surveyed using 14 protocols targeting the soil, litter, understory, lower and upper canopy habitats, replicated across seasons in 2003 and 2004. This dataset is used to explore the relative influence of horizontal, vertical and seasonal drivers of arthropod distribution in this forest. We considered arthropod abundance, observed and estimated species richness, additive decomposition of species richness, multiplicative partitioning of species diversity, variation in species composition, species turnover and guild structure as components of diversity. At the scale of our study (2km of distance, 40m in height and 400 days), the effects related to the vertical and seasonal dimensions were most important. Most adult arthropods were collected from the soil/litter or the upper canopy and species richness was highest in the canopy. We compared the distribution of arthropods and trees within our study system. Effects related to the seasonal dimension were stronger for arthropods than for trees. We conclude that: (1) models of beta diversity developed for tropical trees are unlikely to be applicable to tropical arthropods; (2) it is imperative that estimates of global biodiversity derived from mass collecting of arthropods in tropical rainforests embrace the strong vertical and seasonal partitioning observed here; and (3) given the high species turnover observed between seasons, global climate change may have severe consequences for rainforest arthropods.
KW  - trees
KW  - species richness
KW  - beta-diveristy
KW  - strategy
KW  - turnover
KW  - similarity
KW  - biodiversity
KW  - specialization
KW  - herbivorous insects
KW  - assemblages
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-136393
VL  - 10
IS  - 12
ER  - 
TY  - JOUR
A1  - Bartomeus, Ignasi
A1  - Potts, Simon G.
A1  - Steffan-Dewenter, Ingolf
A1  - Vaissiere, Bernard E.
A1  - Woyciechowski, Michal
A1  - Krewenka, Kristin M.
A1  - Tscheulin, Thomas
A1  - Roberts, Stuart P. M.
A1  - Szentgyoergyi, Hajnalka
A1  - Westphal, Catrin
A1  - Bommarco, Riccardo
T1  - Contribution of insect pollinators to crop yield and quality varies with agricultural intensification
JF  - PEERJ
N2  - Background. Up to 75% of crop species benefit at least to some degree from animal pollination for fruit or seed set and yield. However, basic information on the level of pollinator dependence and pollinator contribution to yield is lacking for many crops. Even less is known about how insect pollination affects crop quality. Given that habitat loss and agricultural intensification are known to decrease pollinator richness and abundance, there is a need to assess the consequences for different components of crop production. Methods. We used pollination exclusion on flowers or inflorescences on a whole plant basis to assess the contribution of insect pollination to crop yield and quality in four flowering crops (spring oilseed rape, field bean, strawberry, and buckwheat) located in four regions of Europe. For each crop, we recorded abundance and species richness of flower visiting insects in ten fields located along a gradient from simple to heterogeneous landscapes. Results. Insect pollination enhanced average crop yield between 18 and 71% depending on the crop. Yield quality was also enhanced in most crops. For instance, oilseed rape had higher oil and lower chlorophyll contents when adequately pollinated, the proportion of empty seeds decreased in buckwheat, and strawberries' commercial grade improved; however, we did not find higher nitrogen content in open pollinated field beans. Complex landscapes had a higher overall species richness of wild pollinators across crops, but visitation rates were only higher in complex landscapes for some crops. On the contrary, the overall yield was consistently enhanced by higher visitation rates, but not by higher pollinator richness. Discussion. For the four crops in this study, there is clear benefit delivered by pollinators on yield quantity and/or quality, but it is not maximized under current agricultural intensification. Honeybees, the most abundant pollinator, might partially compensate the loss of wild pollinators in some areas, but our results suggest the need of landscape-scale actions to enhance wild pollinator populations.
KW  - biodiversity
KW  - pollination
KW  - honeybee
KW  - wild bees
KW  - agroecosystems
KW  - native pollinators
KW  - species richness
KW  - bee pollinators
KW  - wild
KW  - ecosystemservices
KW  - fruit-quality
KW  - oilseed rape
KW  - land-use
KW  - honey
KW  - patterns
Y1  - 2014
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-116928
SN  - 2167-9843
VL  - 2
IS  - e328
ER  - 
TY  - JOUR
A1  - Bartmann, Catharina
A1  - Janaki Raman, Sudha R.
A1  - Flöter, Jessica
A1  - Schulze, Almut
A1  - Bahlke, Katrin
A1  - Willingstorfer, Jana
A1  - Strunz, Maria
A1  - Wöckel, Achim
A1  - Klement, Rainer J.
A1  - Kapp, Michaela
A1  - Djuzenova, Cholpon S.
A1  - Otto, Christoph
A1  - Kämmerer, Ulrike
T1  - Beta-hydroxybutyrate (3-OHB) can influence the energetic phenotype of breast cancer cells, but does not impact their proliferation and the response to chemotherapy or radiation
JF  - Cancer & Metabolism
N2  - Background:
Ketogenic diets (KDs) or short-term fasting are popular trends amongst supportive approaches for cancer patients. Beta-hydroxybutyrate (3-OHB) is the main physiological ketone body, whose concentration can reach plasma levels of 2–6 mM during KDs or fasting. The impact of 3-OHB on the biology of tumor cells described so far is contradictory. Therefore, we investigated the effect of a physiological concentration of 3 mM 3-OHB on metabolism, proliferation, and viability of breast cancer (BC) cells in vitro.

Methods:
Seven different human BC cell lines (BT20, BT474, HBL100, MCF-7, MDA-MB 231, MDA-MB 468, and T47D) were cultured in medium with 5 mM glucose in the presence of 3 mM 3-OHB at mild hypoxia (5% oxygen) or normoxia (21% oxygen). Metabolic profiling was performed by quantification of the turnover of glucose, lactate, and 3-OHB and by Seahorse metabolic flux analysis. Expression of key enzymes of ketolysis as well as the main monocarboxylic acid transporter MCT2 and the glucose-transporter GLUT1 was analyzed by RT-qPCR and Western blotting. The effect of 3-OHB on short- and long-term cell proliferation as well as chemo- and radiosensitivity were also analyzed.

Results:
3-OHB significantly changed the oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) in BT20 cells resulting in a more oxidative energetic phenotype. MCF-7 and MDA-MB 468 cells had increased ECAR only in response to 3-OHB, while the other three cell types remained uninfluenced. All cells expressed MCT2 and GLUT1, thus being able to uptake the metabolites. The consumption of 3-OHB was not strongly linked to mRNA overexpression of key enzymes of ketolysis and did not correlate with lactate production and glucose consumption. Neither 3-OHB nor acetoacetate did interfere with proliferation. Further, 3-OHB incubation did not modify the response of the tested BC cell lines to chemotherapy or radiation.

Conclusions:
We found that a physiological level of 3-OHB can change the energetic profile of some BC cell lines. However, 3-OHB failed to influence different biologic processes in these cells, e.g., cell proliferation and the response to common breast cancer chemotherapy and radiotherapy. Thus, we have no evidence that 3-OHB generally influences the biology of breast cancer cells in vitro.
KW  - ketogenic diet
KW  - β-Hydroxybutyrate
KW  - ketone bodies
KW  - breast cancer
KW  - seahorse
KW  - metabolic profile
KW  - chemotherapy
KW  - ionizing radiation
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-175607
VL  - 6
IS  - 8
ER  - 
TY  - JOUR
A1  - Bartel, Karin
A1  - Pein, Helmut
A1  - Popper, Bastian
A1  - Schmitt, Sabine
A1  - Janaki-Raman, Sudha
A1  - Schulze, Almut
A1  - Lengauer, Florian
A1  - Koeberle, Andreas
A1  - Werz, Oliver
A1  - Zischka, Hans
A1  - Müller, Rolf
A1  - Vollmar, Angelika M.
A1  - Schwarzenberg, Karin von
T1  - Connecting lysosomes and mitochondria – a novel role for lipid metabolism in cancer cell death
JF  - Cell Communication and Signaling
N2  - Background
The understanding of lysosomes has been expanded in recent research way beyond their view as cellular trash can. Lysosomes are pivotal in regulating metabolism, endocytosis and autophagy and are implicated in cancer. Recently it was discovered that the lysosomal V-ATPase, which is known to induce apoptosis, interferes with lipid metabolism in cancer, yet the interplay between these organelles is poorly understood.

Methods
LC-MS/MS analysis was performed to investigate lipid distribution in cells. Cell survival and signaling pathways were analyzed by means of cell biological methods (qPCR, Western Blot, flow cytometry, CellTiter-Blue). Mitochondrial structure was analyzed by confocal imaging and electron microscopy, their function was determined by flow cytometry and seahorse measurements.

Results
Our data reveal that interfering with lysosomal function changes composition and subcellular localization of triacylglycerids accompanied by an upregulation of PGC1α and PPARα expression, master regulators of energy and lipid metabolism. Furthermore, cardiolipin content is reduced driving mitochondria into fission, accompanied by a loss of membrane potential and reduction in oxidative capacity, which leads to a deregulation in cellular ROS and induction of mitochondria-driven apoptosis. Additionally, cells undergo a metabolic shift to glutamine dependency, correlated with the fission phenotype and sensitivity to lysosomal inhibition, most prominent in Ras mutated cells.

Conclusion
This study sheds mechanistic light on a largely uninvestigated triangle between lysosomes, lipid metabolism and mitochondrial function. Insight into this organelle crosstalk increases our understanding of mitochondria-driven cell death. Our findings furthermore provide a first hint on a connection of Ras pathway mutations and sensitivity towards lysosomal inhibitors.
KW  - lysosome
KW  - V-ATPase
KW  - mitochondria
KW  - fission
KW  - apoptosis
KW  - lipid metabolism
KW  - cardiolipin
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-221524
VL  - 17
ER  - 
TY  - JOUR
A1  - Barnekow, Angelika
A1  - Jahn, Reinhard
A1  - Schartl, Manfred
T1  - Synaptophysin: a substrate for the protein tyrosine kinase pp60c-src in intact synaptic vesicles
N2  - Expression of pp60 c-src, the first well defined proto-oncogene product, is developmentally regulated and tissue-specific, with neuronal tissues displaying high amounts of the c-src encoded pp60 c-src kinase activity. In the central nervous system pp60 s-src is preferentially expressed in regions characterized by a high content of grey matter and elevated density of nerve terminals. In this study we show for the first time a direct interaction between pp60 c-src and synaptophysin as a physiological target protein in neurons by demonstrating that endogenous pp60 c-src is able to phosphorylate synaptophysin (p38). p38 is a major constituent of the synaptic vesicle membrane protein and is thought to play a key role in the exocytosis of small synaptic vesicles and possibly small clear vesicles in neuroendocrine cells.
KW  - Synaptophysin
KW  - Synaptische Vesikel
KW  - Protein-Tyrosin-Kinasen
Y1  - 1990
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-86168
ER  - 
TY  - JOUR
A1  - Barnekow, Angelika
A1  - Gessler, Manfred
T1  - Activation of the pp60\(^{c-src}\) kinase during differentiation of monomyelocytic cells in vitro
N2  - Tbe proto-oncogene c-src, the cellular homolog of the Rous sarcoma virus (RSV) transforming gene v-src, is expressed in a tissue-specific and age-dependent manner. Its physiological function, although still unknown, appears to be more closely related to differentiation processes than to proliferation processes. To obtain more information about the physiological role of the c-src gene in cells, we have studied differentiation-dependent alterations using the human HL-60 leukaemia cell line as a model system. Induction of monocytic and granulocytic differentiation of HL-60 cells by 12-0-tetradecanoylphorbol-13-acetate (TPA) and dimethylsulfoxide (DMSO) is associated with an activation of the pp60<sup>c-src</sup> tyrosine kinase, but not with increased c-src gene expression. Control experiments exclude an interaction of TPA and DMSO themselves with the pp60<sup>c-src</sup> kinase.
KW  - Biochemie
KW  - c-src
KW  - differentiation
KW  - protein tyrosine kinase
KW  - protooncogene
Y1  - 1986
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-59278
ER  - 
TY  - JOUR
A1  - Barnekow, A.
A1  - Schartl, Manfred
A1  - Anders, F.
A1  - Bauer, H.
T1  - Identification of a fish protein associated with a kinase activity and related to the Rous sarcoma virus transforming protein
N2  - No abstract available
KW  - Physiologische Chemie
Y1  - 1982
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-61946
ER  - 
TY  - JOUR
A1  - Barnekow, A.
A1  - Schartl, Manfred
T1  - Comparative studies on the src proto-oncogene and its gene product pp60\(^{c-src}\) in normal and neoplastic tissues of lower vertebrates
N2  - No abstract available
KW  - Physiologische Chemie
Y1  - 1987
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-61869
ER  - 
TY  - JOUR
A1  - Barnekow, A.
A1  - Paul, E.
A1  - Schartl, Manfred
T1  - Expression of the c-src protooncogene in human skin tumors
N2  - No abstract available
KW  - Physiologische Chemie
Y1  - 1987
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-61870
ER  - 
TY  - JOUR
A1  - Bargul, Joel L.
A1  - Jung, Jamin
A1  - McOdimba, Francis A.
A1  - Omogo, Collins O.
A1  - Adung'a, Vincent O.
A1  - Krüger, Timothy
A1  - Masiga, Daniel K.
A1  - Engstler, Markus
T1  - Species-Specific Adaptations of Trypanosome Morphology and Motility to the Mammalian Host
JF  - PLoS Pathogens
N2  - African trypanosomes thrive in the bloodstream and tissue spaces of a wide range of mammalian hosts. Infections of cattle cause an enormous socio-economic burden in sub-Saharan Africa. A hallmark of the trypanosome lifestyle is the flagellate’s incessant motion. This work details the cell motility behavior of the four livestock-parasites Trypanosoma vivax, T. brucei, T. evansi and T. congolense. The trypanosomes feature distinct swimming patterns, speeds and flagellar wave frequencies, although the basic mechanism of flagellar propulsion is conserved, as is shown by extended single flagellar beat analyses. Three-dimensional analyses of the trypanosomes expose a high degree of dynamic pleomorphism, typified by the ‘cellular waveform’. This is a product of the flagellar oscillation, the chirality of the flagellum attachment and the stiffness of the trypanosome cell body. The waveforms are characteristic for each trypanosome species and are influenced by changes of the microenvironment, such as differences in viscosity and the presence of confining obstacles. The distinct cellular waveforms may be reflective of the actual anatomical niches the parasites populate within their mammalian host. T. vivax displays waveforms optimally aligned to the topology of the bloodstream, while the two subspecies T. brucei and T. evansi feature distinct cellular waveforms, both additionally adapted to motion in more confined environments such as tissue spaces. T. congolense reveals a small and stiff waveform, which makes these parasites weak swimmers and destined for cell adherence in low flow areas of the circulation. Thus, our experiments show that the differential dissemination and annidation of trypanosomes in their mammalian hosts may depend on the distinct swimming capabilities of the parasites.
KW  - swimming
KW  - viscosity
KW  - flagella
KW  - host-pathogen interactions
KW  - cell motility
KW  - blood
KW  - parasitic diseases
KW  - trypanosoma brucei gambiense
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-146513
VL  - 12
IS  - 2
ER  -