@article{SajkoGrishkovskayaKostanetal.2020, author = {Sajko, Sara and Grishkovskaya, Irina and Kostan, Julius and Graewert, Melissa and Setiawan, Kim and Tr{\"u}bestein, Linda and Niederm{\"u}ller, Korbinian and Gehin, Charlotte and Sponga, Antonio and Puchinger, Martin and Gavin, Anne-Claude and Leonard, Thomas A. and Svergun, Dimitri I. and Smith, Terry K. and Morriswood, Brooke and Djinovic-Carugo, Kristina}, title = {Structures of three MORN repeat proteins and a re-evaluation of the proposed lipid-binding properties of MORN repeats}, series = {PLoS One}, volume = {15}, journal = {PLoS One}, number = {23}, doi = {10.1371/journal.pone.0242677}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-231261}, year = {2020}, abstract = {MORN (Membrane Occupation and Recognition Nexus) repeat proteins have a wide taxonomic distribution, being found in both prokaryotes and eukaryotes. Despite this ubiquity, they remain poorly characterised at both a structural and a functional level compared to other common repeats. In functional terms, they are often assumed to be lipid-binding modules that mediate membrane targeting. We addressed this putative activity by focusing on a protein composed solely of MORN repeats-Trypanosoma brucei MORN1. Surprisingly, no evidence for binding to membranes or lipid vesicles by TbMORN1 could be obtained either in vivo or in vitro. Conversely, TbMORN1 did interact with individual phospholipids. High- and low-resolution structures of the MORN1 protein from Trypanosoma brucei and homologous proteins from the parasites Toxoplasma gondii and Plasmodium falciparum were obtained using a combination of macromolecular crystallography, small-angle X-ray scattering, and electron microscopy. This enabled a first structure-based definition of the MORN repeat itself. Furthermore, all three structures dimerised via their C-termini in an antiparallel configuration. The dimers could form extended or V-shaped quaternary structures depending on the presence of specific interface residues. This work provides a new perspective on MORN repeats, showing that they are protein-protein interaction modules capable of mediating both dimerisation and oligomerisation.}, language = {en} } @article{GoetzKunzFinketal.2020, author = {G{\"o}tz, Ralph and Kunz, Tobias C. and Fink, Julian and Solger, Franziska and Schlegel, Jan and Seibel, J{\"u}rgen and Kozjak-Pavlovic, Vera and Rudel, Thomas and Sauer, Markus}, title = {Nanoscale imaging of bacterial infections by sphingolipid expansion microscopy}, series = {Nature Communications}, volume = {11}, journal = {Nature Communications}, doi = {10.1038/s41467-020-19897-1}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-231248}, year = {2020}, abstract = {Expansion microscopy (ExM) enables super-resolution imaging of proteins and nucleic acids on conventional microscopes. However, imaging of details of the organization of lipid bilayers by light microscopy remains challenging. We introduce an unnatural short-chain azide- and amino-modified sphingolipid ceramide, which upon incorporation into membranes can be labeled by click chemistry and linked into hydrogels, followed by 4x to 10x expansion. Confocal and structured illumination microscopy (SIM) enable imaging of sphingolipids and their interactions with proteins in the plasma membrane and membrane of intracellular organelles with a spatial resolution of 10-20nm. As our functionalized sphingolipids accumulate efficiently in pathogens, we use sphingolipid ExM to investigate bacterial infections of human HeLa229 cells by Neisseria gonorrhoeae, Chlamydia trachomatis and Simkania negevensis with a resolution so far only provided by electron microscopy. In particular, sphingolipid ExM allows us to visualize the inner and outer membrane of intracellular bacteria and determine their distance to 27.6 +/- 7.7nm. Imaging of lipid bilayers using light microscopy is challenging. Here the authors label cells using a short chain click-compatible ceramide to visualize mammalian and bacterial membranes with expansion microscopy.}, language = {en} } @article{MarkertSkoruppaYuetal.2020, author = {Markert, Sebastian M. and Skoruppa, Michael and Yu, Bin and Mulcahy, Ben and Zhen, Mai and Gao, Shangbang and Sendtner, Michael and Stigloher, Christian}, title = {Overexpression of an ALS-associated FUS mutation in C. elegans disrupts NMJ morphology and leads to defective neuromuscular transmission}, series = {Biology Open}, volume = {9}, journal = {Biology Open}, doi = {10.1242/bio.055129}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-230662}, year = {2020}, abstract = {The amyotrophic lateral sclerosis (ALS) neurodegenerative disorder has been associated with multiple genetic lesions, including mutations in the gene for fused in sarcoma (FUS), a nuclear-localized RNA/DNA-binding protein. Neuronal expression of the pathological form of FUS proteins in Caenorhabditis elegans results in mislocalization and aggregation of FUS in the cytoplasm, and leads to impairment of motility. However, the mechanisms by which the mutant FUS disrupts neuronal health and function remain unclear. Here we investigated the impact of ALS-associated FUS on motor neuron health using correlative light and electron microscopy, electron tomography, and electrophysiology. We show that ectopic expression of wild-type or ALS-associated human FUS impairs synaptic vesicle docking at neuromuscular junctions. ALS-associated FUS led to the emergence of a population of large, electron-dense, and filament-filled endosomes. Electrophysiological recording revealed reduced transmission from motor neurons to muscles. Together, these results suggest a pathological effect of ALS-causing FUS at synaptic structure and function organization.}, language = {en} } @article{VogelGossnerMergneretal.2020, author = {Vogel, Sebastian and Gossner, Martin M. and Mergner, Ulrich and M{\"u}ller, J{\"o}rg and Thorn, Simon}, title = {Optimizing enrichment of deadwood for biodiversity by varying sun exposure and tree species: An experimental approach}, series = {Journal of Applied Ecology}, volume = {57}, journal = {Journal of Applied Ecology}, number = {10}, doi = {10.1111/1365-2664.13648}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-214614}, pages = {2075 -- 2085}, year = {2020}, abstract = {The enrichment of deadwood is essential for the conservation of saproxylic biodiversity in managed forests. However, existing strategies focus on a cost-intensive increase of deadwood amount, while largely neglecting increasing deadwood diversity. Deadwood objects, that is logs and branches, from six tree species were experimentally sun exposed, canopy shaded and artificially shaded for 4 years, after which the alpha-, beta- and gamma-diversity of saproxylic beetles, wood-inhabiting fungi and spiders were analysed. Analyses of beta-diversity included the spatial distance between exposed deadwood objects. A random-drawing procedure was used to identify the combination of tree species and sun exposure that yielded the highest gamma-diversity at a minimum of exposed deadwood amount. In sun-exposed plots, species numbers in logs were higher than in shaded plots for all taxa, while in branches we observed the opposite for saproxylic beetles. Tree species affected the species numbers only of saproxylic beetles and wood-inhabiting fungi. The beta-diversity of saproxylic beetles and wood-inhabiting fungi among logs was influenced by sun exposure and tree species, but beta-diversity of spiders by sun exposure only. For all saproxylic taxa recorded in logs, differences between communities increased with increasing spatial distance. A combination of canopy-shaded Carpinus logs and sun-exposed Populus logs resulted in the highest species numbers of all investigated saproxylic taxa among all possible combinations of tree species and sun-exposure treatments. Synthesis and applications. We recommend incorporating the enrichment of different tree species and particularly the variation in sun exposure into existing strategies of deadwood enrichment. Based on the results of our study, we suggest to combine the logs of softwood broadleaf tree species (e.g. Carpinus, Populus), hardwood broadleaf tree species (e.g. Quercus) and coniferous tree species (e.g. Pinus) under different conditions of sun exposure and distribute them spatially in a landscape to maximize the beneficial effects on overall diversity.}, language = {en} } @article{LealSchwebsBriggsetal.2020, author = {Leal, Andrea Zurita and Schwebs, Marie and Briggs, Emma and Weisert, Nadine and Reis, Helena and Lemgruber, Leondro and Luko, Katarina and Wilkes, Jonathan and Butter, Falk and McCulloch, Richard and Janzen, Christian J.}, title = {Genome maintenance functions of a putative Trypanosoma brucei translesion DNA polymerase include telomere association and a role in antigenic variation}, series = {Nucleic Acids Research}, volume = {48}, journal = {Nucleic Acids Research}, number = {17}, doi = {10.1093/nar/gkaa686}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-230579}, pages = {9660-9680}, year = {2020}, abstract = {Maintenance of genome integrity is critical to guarantee transfer of an intact genome from parent to off-spring during cell division. DNA polymerases (Pols) provide roles in both replication of the genome and the repair of a wide range of lesions. Amongst replicative DNA Pols, translesion DNA Pols play a particular role: replication to bypass DNA damage. All cells express a range of translesion Pols, but little work has examined their function in parasites, including whether the enzymes might contribute to host-parasite interactions. Here, we describe a dual function of one putative translesion Pol in African trypanosomes, which we now name TbPolIE. Previously, we demonstrated that TbPolIE is associated with telomeric sequences and here we show that RNAi-mediated depletion of TbPolIE transcripts results in slowed growth, altered DNA content, changes in cell morphology, and increased sensitivity to DNA damaging agents. We also show that TbPolIE displays pronounced localization at the nuclear periphery, and that its depletion leads to chromosome segregation defects and increased levels of endogenous DNA damage. Finally, we demonstrate that TbPolIE depletion leads to deregulation of telomeric variant surface glycoprotein genes, linking the function of this putative translesion DNA polymerase to host immune evasion by antigenic variation.}, language = {en} } @article{FlorenvonRintelenHerbertetal.2020, author = {Floren, Andreas and von Rintelen, Thomas and Herbert, Paul D. N. and de Araujo, Bruno Cancian and Schmidt, Stefan and Balke, Michael and Narakusumo, Raden Pramesa and Peggie, Djunijanti and Ubaidillah, Rosichon and von Rintelen, Kristina and M{\"u}ller, Tobias}, title = {Integrative ecological and molecular analysis indicate high diversity and strict elevational separation of canopy beetles in tropical mountain forests}, series = {Scientific Reports}, volume = {10}, journal = {Scientific Reports}, doi = {10.1038/s41598-020-73519-w}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-230565}, year = {2020}, abstract = {Tropical mountain forests contribute disproportionately to terrestrial biodiversity but little is known about insect diversity in the canopy and how it is distributed between tree species. We sampled tree-specific arthropod communities from 28 trees by canopy fogging and analysed beetle communities which were first morphotyped and then identified by their DNA barcodes. Our results show that communities from forests at 1100 and 1700 m a.s.l. are almost completely distinct. Diversity was much lower in the upper forest while community structure changed from many rare, less abundant species to communities with a pronounced dominance structure. We also found significantly higher beta-diversity between trees at the lower than higher elevation forest where community similarity was high. Comparisons on tree species found at both elevations reinforced these results. There was little species overlap between sites indicating limited elevational ranges. Furthermore, we exploited the advantage of DNA barcodes to patterns of haplotype diversity in some of the commoner species. Our results support the advantage of fogging and DNA barcodes for community studies and underline the need for comprehensive research aimed at the preservation of these last remaining pristine forests.}, language = {en} } @article{MatthesDiersSchlegeletal.2020, author = {Matthes, Niels and Diers, Johannes and Schlegel, Nicolas and Hankir, Mohammed and Haubitz, Imme and Germer, Christoph-Thomas and Wiegering, Armin}, title = {Validation of MTL30 as a quality indicator for colorectal surgery}, series = {PLoS One}, volume = {15}, journal = {PLoS One}, number = {8}, doi = {10.1371/journal.pone.0238473}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-230530}, year = {2020}, abstract = {Background Valid indicators are required to measure surgical quality. These ideally should be sensitive and selective while being easy to understand and adjust. We propose here the MTL30 quality indicator which takes into account 30-day mortality, transfer within 30 days, and a length of stay of 30 days as composite markers of an uneventful operative/postoperative course. Methods Patients documented in the StuDoQ|Colon and StuDoQ|Rectal carcinoma register of the German Society for General and Visceral Surgery (DGAV) were analyzed with regard to the effects of patient and tumor-related risk factors as well as postoperative complications on the MTL30. Results In univariate analysis, the MTL30 correlated significantly with patient and tumor-related risk factors such as ASA score (p<0.001), age (p<0.001), or UICC stage (p<0.001). There was a high sensitivity for the postoperative occurrence of complications such as re-operations (p<0.001) or subsequent bleeding (p<0.001), as well as a significant correlation with the CDC classification (p<0.001). In multivariate analysis, patient-related risk factors and postoperative complications significantly increased the odds ratio for a positive MTL30. A negative MTL30 showed a high specify for an uneventful operative and postoperative course. Conclusion The MTL30 is a valid indicator of colorectal surgical quality.}, language = {en} } @article{ThornChaoGeorgievetal.2020, author = {Thorn, Simon and Chao, Anne and Georgiev, Konstadin B. and M{\"u}ller, J{\"o}rg and B{\"a}ssler, Claus and Campbell, John L. and Jorge, Castro and Chen, Yan-Han and Choi, Chang-Yong and Cobb, Tyler P. and Donato, Daniel C. and Durska, Ewa and Macdonald, Ellen and Feldhaar, Heike and Fontaine, Jospeh B. and Fornwalt, Paula J. and Hern{\´a}ndez Hern{\´a}ndez, Raquel Mar{\´i}a and Hutto, Richard L. and Koivula, Matti and Lee, Eun-Jae and Lindenmayer, David and Mikusinski, Grzegorz and Obrist, Martin K. and Perl{\´i}k, Michal and Rost, Josep and Waldron, Kaysandra and Wermelinger, Beat and Weiß, Ingmar and Zmihorski, Michal and Leverkus, Alexandro B.}, title = {Estimating retention benchmarks for salvage logging to protect biodiversity}, series = {Nature Communications}, volume = {11}, journal = {Nature Communications}, doi = {10.1038/s41467-020-18612-4}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-230512}, year = {2020}, abstract = {Forests are increasingly affected by natural disturbances. Subsequent salvage logging, a widespread management practice conducted predominantly to recover economic capital, produces further disturbance and impacts biodiversity worldwide. Hence, naturally disturbed forests are among the most threatened habitats in the world, with consequences for their associated biodiversity. However, there are no evidence-based benchmarks for the proportion of area of naturally disturbed forests to be excluded from salvage logging to conserve biodiversity. We apply a mixed rarefaction/extrapolation approach to a global multi-taxa dataset from disturbed forests, including birds, plants, insects and fungi, to close this gap. We find that 757\% (mean +/- SD) of a naturally disturbed area of a forest needs to be left unlogged to maintain 90\% richness of its unique species, whereas retaining 50\% of a naturally disturbed forest unlogged maintains 73 +/- 12\% of its unique species richness. These values do not change with the time elapsed since disturbance but vary considerably among taxonomic groups. Salvage logging has become a common practice to gain economic returns from naturally disturbed forests, but it could have considerable negative effects on biodiversity. Here the authors use a recently developed statistical method to estimate that ca. 75\% of the naturally disturbed forest should be left unlogged to maintain 90\% of the species unique to the area.}, language = {en} } @article{GromaHorstDasetal.2020, author = {Groma, Michaela and Horst, Sarah A. and Das, Sudip and Huettel, Bruno and Klepsch, Maximilian and Rudel, Thomas and Medina, Eva and Fraunholz, Martin}, title = {Identification of a Novel LysR-Type Transcriptional Regulator in Staphylococcus aureus That Is Crucial for Secondary Tissue Colonization during Metastatic Bloodstream Infection}, series = {mbio}, volume = {11}, journal = {mbio}, number = {4}, doi = {10.1128/mBio.01646-20}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-230473}, year = {2020}, abstract = {Staphylococcus aureus is a common cause of bacteremia that can lead to severe complications once the bacteria exit the bloodstream and establish infection in secondary organs. Despite its clinical relevance, little is known about the bacterial factors facilitating the development of these metastatic infections. Here, we used an S. aureus transposon mutant library coupled to transposon insertion sequencing (Tn-Seq) to identify genes that are critical for efficient bacterial colonization of secondary organs in a murine model of metastatic bloodstream infection. Our transposon screen identified a LysR-type transcriptional regulator (LTTR), which was required for efficient colonization of secondary organs such as the kidneys in infected mice. The critical role of LTTR in secondary organ colonization was confirmed using an isogenic mutant deficient in the expression of LTTR. To identify the set of genes controlled by LTTR, we used an S. aureus strain carrying the LTTR gene in an inducible expression plasmid. Gene expression analysis upon induction of LTTR showed increased transcription of genes involved in branched-chain amino acid biosynthesis, a methionine sulfoxide reductase, and a copper transporter as well as decreased transcription of genes coding for urease and components of pyrimidine nucleotides. Furthermore, we show that transcription of LTTR is repressed by glucose, is induced under microaerobic conditions, and required trace amounts of copper ions. Our data thus pinpoints LTTR as an important element that enables a rapid adaptation of S. aureus to the changing host microenvironment. IMPORTANCE Staphylococcus aureus is an important pathogen that can disseminate via the bloodstream and establish metastatic infections in distant organs. To achieve a better understanding of the bacterial factors facilitating the development of these metastatic infections, we used in this study a Staphylococcus aureus transposon mutant library in a murine model of intravenous infection, where bacteria first colonize the liver as the primary infection site and subsequently progress to secondary sites such as the kidney and bones. We identified a novel LysR-type transcriptional regulator (LTTR), which was specifically required by S. aureus for efficient colonization of secondary organs. We also determined the transcriptional activation as well as the regulon of LTTR, which suggests that this regulator is involved in the metabolic adaptation of S. aureus to the host microenvironment found in secondary infection sites.}, language = {en} } @article{RoemerCosarinskyRoces2020, author = {R{\"o}mer, Daniela and Cosarinsky, Marcela I. and Roces, Flavio}, title = {Selection and spatial arrangement of building materials during the construction of nest turrets by grass-cutting ants}, series = {Royal Society Open Science}, volume = {7}, journal = {Royal Society Open Science}, doi = {10.1098/rsos.201312}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-230458}, year = {2020}, abstract = {Ants build complex nest structures by reacting to simple, local stimuli. While underground nests result from the space generated by digging, some leaf- and grass-cutting ants also construct conspicuous aboveground turrets around nest openings. We investigated whether the selection of specific building materials occurs during turret construction in Acromyrmex fracticornis grass-cutting ants, and asked whether single building decisions at the beginning can modify the final turret architecture. To quantify workers' material selection, the original nest turret was removed and a choice between two artificial building materials, thin and thick sticks, was offered for rebuilding. Workers preferred thick sticks at the very beginning of turret construction, showed varying preferences thereafter, and changed to prefer thin sticks for the upper, final part of the turret, indicating that they selected different building materials over time to create a stable structure. The impact of a single building choice on turret architecture was evaluated by placing artificial beams that divided a colony's nest entrance at the beginning of turret rebuilding. Splitting the nest entrance led to the self-organized construction of turrets with branched galleries ending in multiple openings, showing that the spatial location of a single building material can strongly influence turret morphology.}, language = {en} } @article{WhisnantJuergesHennigetal.2020, author = {Whisnant, Adam W. and J{\"u}rges, Christopher S. and Hennig, Thomas and Wyler, Emanuel and Prusty, Bhupesh and Rutkowski, Andrzej J. and L'hernault, Anne and Djakovic, Lara and G{\"o}bel, Margarete and D{\"o}ring, Kristina and Menegatti, Jennifer and Antrobus, Robin and Matheson, Nicholas J. and K{\"u}nzig, Florian W. H. and Mastrobuoni, Guido and Bielow, Chris and Kempa, Stefan and Liang, Chunguang and Dandekar, Thomas and Zimmer, Ralf and Landthaler, Markus and Gr{\"a}sser, Friedrich and Lehner, Paul J. and Friedel, Caroline C. and Erhard, Florian and D{\"o}lken, Lars}, title = {Integrative functional genomics decodes herpes simplex virus 1}, series = {Nature Communications}, volume = {11}, journal = {Nature Communications}, doi = {10.1038/s41467-020-15992-5}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229884}, year = {2020}, abstract = {The predicted 80 open reading frames (ORFs) of herpes simplex virus 1 (HSV-1) have been intensively studied for decades. Here, we unravel the complete viral transcriptome and translatome during lytic infection with base-pair resolution by computational integration of multi-omics data. We identify a total of 201 transcripts and 284 ORFs including all known and 46 novel large ORFs. This includes a so far unknown ORF in the locus deleted in the FDA-approved oncolytic virus Imlygic. Multiple transcript isoforms expressed from individual gene loci explain translation of the vast majority of ORFs as well as N-terminal extensions (NTEs) and truncations. We show that NTEs with non-canonical start codons govern the subcellular protein localization and packaging of key viral regulators and structural proteins. We extend the current nomenclature to include all viral gene products and provide a genome browser that visualizes all the obtained data from whole genome to single-nucleotide resolution. Here, using computational integration of multi-omics data, the authors provide a detailed transcriptome and translatome of herpes simplex virus 1 (HSV-1), including previously unidentified ORFs and N-terminal extensions. The study also provides a HSV-1 genome browser and should be a valuable resource for further research.}, language = {en} } @article{RothZoderZamanetal.2020, author = {Roth, Nicolas and Zoder, Sebastian and Zaman, Assad Ali and Thorn, Simon and Schmidl, J{\"u}rgen}, title = {Long-term monitoring reveals decreasing water beetle diversity, loss of specialists and community shifts over the past 28 years}, series = {Insect Conservation and Diversity}, volume = {13}, journal = {Insect Conservation and Diversity}, number = {2}, doi = {10.1111/icad.12411}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-214905}, pages = {140 -- 150}, year = {2020}, abstract = {Lentic freshwater organisms are influenced by a multitude of factors, including geomorphology, hydrology, anthropogenic impacts and climate change. Organisms that depend on patchy resources such as water beetles may also be sensitive to anthropogenic habitat degradation, like pollution, eutrophication, water level or management alteration. To assess composition and ecological trends in the water beetle communities of Central Europe, we sampled water beetles (Dytiscidae, Haliplidae, Noteridae) in 33 water bodies in Southern Germany from 1991 to 2018. We used manual, time-standardised capture during three periods: between 1991 and 1995, 2007 and 2008, and 2017 and 2018. During the 28-year survey period, we captured a total of 81 species. We found annual declines in both species number (ca -1\%) and abundance (ca -2\%). Also, community composition showed significant changes over time. The significant impact of pH on the community composition suggests that the recorded changes through time partly reflect natural succession processes. However, a pronounced decline of beetle species belonging to the moor-related beetle associations indicated that Central European water beetles are also threatened by non-successional factors, including desiccation, increased nitrogen input and/or mineralisation, and the loss of specific habitats. This trend to physiographical homogenisation resulted in corresponding community composition shifts. To effectively protect endangered species, conservation strategies need to be aimed at regularly creating new water bodies with mineralic bottom substratum, and maintenance of moor water bodies that represent late successional stages.}, language = {en} } @article{GeorgievChaoCastroetal.2020, author = {Georgiev, Kostadin B. and Chao, Anne and Castro, Jorge and Chen, Yan-Han and Choi, Chang-Yong and Fontaine, Joseph B. and Hutto, Richard L. and Lee, Eun-Jae and M{\"u}ller, J{\"o}rg and Rost, Josep and Żmihorski, Michal and Thorn, Simon}, title = {Salvage logging changes the taxonomic, phylogenetic and functional successional trajectories of forest bird communities}, series = {Journal of Applied Ecology}, volume = {57}, journal = {Journal of Applied Ecology}, number = {6}, doi = {10.1111/1365-2664.13599}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-214887}, pages = {1103 -- 1112}, year = {2020}, abstract = {Salvage logging following natural disturbances may alter the natural successional trajectories of biological communities by affecting the occurrences of species, functional groups and evolutionary lineages. However, few studies have examined whether dissimilarities between bird communities of salvaged and unsalvaged forests are more pronounced for rare species, functional groups and evolutionary lineages than for their more common counterparts. We compiled data on breeding bird assemblages from nine study areas in North America, Europe and Asia, covering a 17-year period following wildfire or windstorm disturbances and subsequent salvage logging. We tested whether dissimilarities based on non-shared species, functional groups and evolutionary lineages (a) decreased or increased over time and (b) the responses of rare, common and dominant species varied, by using a unified statistical framework based on Hill numbers and null models. We found that dissimilarities between bird communities caused by salvage logging persisted over time for rare, common and dominant species, evolutionary lineages and for rare functional groups. Dissimilarities of common and dominant functional groups increased 14 years post disturbance. Salvage logging led to significantly larger dissimilarities than expected by chance. Functional dissimilarities between salvaged and unsalvaged sites were lower compared to taxonomic and phylogenetic dissimilarities. In general, dissimilarities were highest for rare, followed by common and dominant species. Synthesis and applications. Our research demonstrates that salvage logging did not decrease dissimilarities of bird communities over time and taxonomic, functional and phylogenetic dissimilarities persisted for over a decade. We recommend resource managers and decision makers to reserve portions of disturbed forest to enable unmanaged post-disturbance succession of bird communities, particularly to conserve rare species found in unsalvaged disturbed forests.}, language = {en} } @article{GuptaSrivastavaOsmanogluetal.2020, author = {Gupta, Shishir K. and Srivastava, Mugdha and Osmanoglu, Oezge and Dandekar, Thomas}, title = {Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs}, series = {Scientific Reports}, volume = {10}, journal = {Scientific Reports}, number = {1}, doi = {10.1038/s41598-020-59344-1}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229406}, year = {2020}, abstract = {Apart from some model organisms, the interactome of most organisms is largely unidentified. High-throughput experimental techniques to determine protein-protein interactions (PPIs) are resource intensive and highly susceptible to noise. Computational methods of PPI determination can accelerate biological discovery by identifying the most promising interacting pairs of proteins and by assessing the reliability of identified PPIs. Here we present a first in-depth study describing a global view of the ant Camponotus floridanus interactome. Although several ant genomes have been sequenced in the last eight years, studies exploring and investigating PPIs in ants are lacking. Our study attempts to fill this gap and the presented interactome will also serve as a template for determining PPIs in other ants in future. Our C. floridanus interactome covers 51,866 non-redundant PPIs among 6,274 proteins, including 20,544 interactions supported by domain-domain interactions (DDIs), 13,640 interactions supported by DDIs and subcellular localization, and 10,834 high confidence interactions mediated by 3,289 proteins. These interactions involve and cover 30.6\% of the entire C. floridanus proteome.}, language = {en} } @article{LichthardtWagnerLoebetal.2020, author = {Lichthardt, Sven and Wagner, Johanna and L{\"o}b, Stefan and Matthes, Niels and Kastner, Caroline and Anger, Friedrich and Germer, Christoph-Thomas and Wiegering, Armin}, title = {Pathological complete response due to a prolonged time interval between preoperative chemoradiation and surgery in locally advanced rectal cancer: analysis from the German StuDoQ|Rectalcarcinoma registry}, series = {BMC Cancer}, volume = {20}, journal = {BMC Cancer}, number = {1}, doi = {10.1186/s12885-020-6538-8}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229334}, year = {2020}, abstract = {Background Preoperative chemoradiotherapy is the recommended standard of care for patients with local advanced rectal cancer. However, it remains unclear, whether a prolonged time interval to surgery results in an increased perioperative morbidity, reduced TME quality or better pathological response. Aim of this study was to determine the time interval for best pathological response and perioperative outcome compared to current recommended interval of 6 to 8 weeks. Methods This is a retrospective analysis of the German StuDoQ|Rectalcarcinoma registry. Patients were grouped for the time intervals of "less than 6 weeks", "6 to 8 weeks", "8 to 10 weeks" and "more than 10 weeks". Primary endpoint was pathological response, secondary endpoint TME quality and complications according to Clavien-Dindo classification. Results Due to our inclusion criteria (preoperative chemoradiation, surgery in curative intention, M0), 1.809 of 9.560 patients were suitable for analysis. We observed a trend for increased rates of pathological complete response (pCR: ypT0ypN0) and pathological good response (pGR: ypT0-1ypN0) for groups with a prolonged time interval which was not significant. Ultimately, it led to a steady state of pCR (16.5\%) and pGR (22.6\%) in "8 to 10" and "more than 10" weeks. We were not able to observe any differences between the subgroups in perioperative morbidity, proportion of rectal extirpation (for cancer of the lower third) or difference in TME quality. Conclusion A prolonged time interval between neoadjuvant chemoradiation can be performed, as the rate of pCR seems to be increased without influencing perioperative morbidity.}, language = {en} } @article{OsmanStigloherMuelleretal.2020, author = {Osman, Mohamed and Stigloher, Christian and Mueller, Martin J. and Waller, Frank}, title = {An improved growth medium for enhanced inoculum production of the plant growth-promoting fungus Serendipita indica}, series = {Plant Methods}, volume = {16}, journal = {Plant Methods}, doi = {10.1186/s13007-020-00584-7}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229186}, year = {2020}, abstract = {Background The plant endophytic fungus Serendipita indica colonizes roots of a wide range of plant species and can enhance growth and stress resistance of these plants. Due to its ease of axenic cultivation and its broad host plant range including the model plant Arabidopsis thaliana and numerous crop plants, it is widely used as a model fungus to study beneficial fungus-root interactions. In addition, it was suggested to be utilized for commercial applications, e.g. to enhance yield in barley and other species. To produce inoculum, S. indica is mostly cultivated in a complex Hill-Kafer medium (CM medium), however, growth in this medium is slow, and yield of chlamydospores, which are often used for plant root inoculation, is relatively low. Results We tested and optimized a simple vegetable juice-based medium for an enhanced yield of fungal inoculum. The described vegetable juice (VJ) medium is based on commercially available vegetable juice and is easy to prepare. VJ medium was superior to the currently used CM medium with respect to biomass production in liquid medium and hyphal growth on agar plates. Using solid VJ medium supplemented with sucrose (VJS), a high amount of chlamydospores developed already after 8 days of cultivation, producing significantly more spores than on CM medium. Use of VJ medium is not restricted to S. indica, as it also supported growth of two pathogenic fungi often used in plant pathology experiments: the ascomycete Fusarium graminearum, the causal agent of Fusarium head blight disease on wheat and barley, and Verticillium longisporum, the causal agent of verticillium wilt. Conclusions The described VJ medium is recommended for streamlined and efficient production of inoculum for the plant endophytic fungus Serendipita indica and might prove superior for the propagation of other fungi for research purposes.}, language = {en} } @article{ShityakovBencurovaFoersteretal.2020, author = {Shityakov, Sergey and Bencurova, Elena and F{\"o}rster, Carola and Dandekar, Thomas}, title = {Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches}, series = {BMC Bioinformatics}, volume = {2020}, journal = {BMC Bioinformatics}, doi = {10.1186/s12859-020-3461-6}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229169}, year = {2020}, abstract = {Background Processing and analysis of DNA sequences obtained from next-generation sequencing (NGS) face some difficulties in terms of the correct prediction of DNA sequencing outcomes without the implementation of bioinformatics approaches. However, algorithms based on NGS perform inefficiently due to the generation of long DNA fragments, the difficulty of assembling them and the complexity of the used genomes. On the other hand, the Sanger DNA sequencing method is still considered to be the most reliable; it is a reliable choice for virtual modeling to build all possible consensus sequences from smaller DNA fragments. Results In silico and in vitro experiments were conducted: (1) to implement and test our novel sequencing algorithm, using the standard cloning vectors of different length and (2) to validate experimentally virtual shotgun sequencing using the PCR technique with the number of cycles from 1 to 9 for each reaction. Conclusions We applied a novel algorithm based on Sanger methodology to correctly predict and emphasize the performance of DNA sequencing techniques as well as in de novo DNA sequencing and its further application in synthetic biology. We demonstrate the statistical significance of our results.}, language = {en} } @article{MemmelSisarioZimmermannetal.2020, author = {Memmel, Simon and Sisario, Dmitri and Zimmermann, Heiko and Sauer, Markus and Sukhorukov, Vladimir L. and Djuzenova, Cholpon S. and Flentje, Michael}, title = {FocAn: automated 3D analysis of DNA repair foci in image stacks acquired by confocal fluorescence microscopy}, series = {BMC Bioinformatics}, volume = {21}, journal = {BMC Bioinformatics}, doi = {10.1186/s12859-020-3370-8}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229023}, year = {2020}, abstract = {Background Phosphorylated histone H2AX, also known as gamma H2AX, forms mu m-sized nuclear foci at the sites of DNA double-strand breaks (DSBs) induced by ionizing radiation and other agents. Due to their specificity and sensitivity, gamma H2AX immunoassays have become the gold standard for studying DSB induction and repair. One of these assays relies on the immunofluorescent staining of gamma H2AX followed by microscopic imaging and foci counting. During the last years, semi- and fully automated image analysis, capable of fast detection and quantification of gamma H2AX foci in large datasets of fluorescence images, are gradually replacing the traditional method of manual foci counting. A major drawback of the non-commercial software for foci counting (available so far) is that they are restricted to 2D-image data. In practice, these algorithms are useful for counting the foci located close to the midsection plane of the nucleus, while the out-of-plane foci are neglected. Results To overcome the limitations of 2D foci counting, we present a freely available ImageJ-based plugin (FocAn) for automated 3D analysis of gamma H2AX foci in z-image stacks acquired by confocal fluorescence microscopy. The image-stack processing algorithm implemented in FocAn is capable of automatic 3D recognition of individual cell nuclei and gamma H2AX foci, as well as evaluation of the total foci number per cell nucleus. The FocAn algorithm consists of two parts: nucleus identification and foci detection, each employing specific sequences of auto local thresholding in combination with watershed segmentation techniques. We validated the FocAn algorithm using fluorescence-labeled gamma H2AX in two glioblastoma cell lines, irradiated with 2 Gy and given up to 24 h post-irradiation for repair. We found that the data obtained with FocAn agreed well with those obtained with an already available software (FoCo) and manual counting. Moreover, FocAn was capable of identifying overlapping foci in 3D space, which ensured accurate foci counting even at high DSB density of up to similar to 200 DSB/nucleus. Conclusions FocAn is freely available an open-source 3D foci analyzer. The user-friendly algorithm FocAn requires little supervision and can automatically count the amount of DNA-DSBs, i.e. fluorescence-labeled gamma H2AX foci, in 3D image stacks acquired by laser-scanning microscopes without additional nuclei staining.}, language = {en} } @article{BowlerBjorkmanDornelasetal.2020, author = {Bowler, Diana E. and Bjorkman, Anne D. and Dornelas, Maria and Myers-Smith, Isla H. and Navarro, Laetitia M. and Niamir, Aidin and Supp, Sarah R. and Waldock, Conor and Winter, Marten and Vellend, Mark and Blowes, Shane A. and B{\"o}hning-Gaese, Katrin and Bruelheide, Helge and Elahi, Robin and Ant{\~a}o, Laura H. and Hines, Jes and Isbell, Forest and Jones, Holly P. and Magurran, Anne E. and Cabral, Juliano Sarmento and Bates, Amanda E.}, title = {Mapping human pressures on biodiversity across the planet uncovers anthropogenic threat complexes}, series = {People and Nature}, volume = {2}, journal = {People and Nature}, number = {2}, doi = {10.1002/pan3.10071}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-213634}, pages = {380 -- 394}, year = {2020}, abstract = {Climate change and other anthropogenic drivers of biodiversity change are unequally distributed across the world. Overlap in the distributions of different drivers have important implications for biodiversity change attribution and the potential for interactive effects. However, the spatial relationships among different drivers and whether they differ between the terrestrial and marine realm has yet to be examined. We compiled global gridded datasets on climate change, land-use, resource exploitation, pollution, alien species potential and human population density. We used multivariate statistics to examine the spatial relationships among the drivers and to characterize the typical combinations of drivers experienced by different regions of the world. We found stronger positive correlations among drivers in the terrestrial than in the marine realm, leading to areas with high intensities of multiple drivers on land. Climate change tended to be negatively correlated with other drivers in the terrestrial realm (e.g. in the tundra and boreal forest with high climate change but low human use and pollution), whereas the opposite was true in the marine realm (e.g. in the Indo-Pacific with high climate change and high fishing). We show that different regions of the world can be defined by Anthropogenic Threat Complexes (ATCs), distinguished by different sets of drivers with varying intensities. We identify 11 ATCs that can be used to test hypotheses about patterns of biodiversity and ecosystem change, especially about the joint effects of multiple drivers. Our global analysis highlights the broad conservation priorities needed to mitigate the impacts of anthropogenic change, with different priorities emerging on land and in the ocean, and in different parts of the world.}, language = {en} } @article{BeerHelfrichFoerster2020, author = {Beer, Katharina and Helfrich-F{\"o}rster, Charlotte}, title = {Model and Non-model Insects in Chronobiology}, series = {Frontiers in Behavioral Neuroscience}, volume = {14}, journal = {Frontiers in Behavioral Neuroscience}, issn = {1662-5153}, doi = {10.3389/fnbeh.2020.601676}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-218721}, year = {2020}, abstract = {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.}, language = {en} }