@article{KrajinovicReimerKudlichetal.2016,
  author    = {Krajinovic, K. and Reimer, S. and Kudlich, T. and Germer, C. T. and Wiegering, A.},
  title     = {"Rendezvous technique" for intraluminal vacuum therapy of anastomotic leakage of the jejunum},
  series = {Surgical Case Reports},
  volume    = {2},
  journal   = {Surgical Case Reports},
  number    = {114},
  doi       = {10.1186/s40792-016-0243-5},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147883},
  year      = {2016},
  abstract  = {Background Anastomotic leakage (AL) is one of the most common and serious complications following visceral surgery. In recent years, endoluminal vacuum therapy has dramatically changed therapeutic options for AL, but its use has been limited to areas easily accessible by endoscope. Case presentation We describe the first use of endoluminal vacuum therapy in the small intestine employing a combined surgical and endoscopic "rendezvous technique" in which the surgeon assists the endoscopic placement of an endoluminal vacuum therapy sponge in the jejunum by means of a pullback string. This technique led to a completely closed AL after 27 days and 7 changes of the endosponge. Conclusion The combined surgical and endoscopic rendezvous technique can be useful in cases of otherwise difficult endosponge placement.},
  language  = {en}
}
@article{ShenChalopinGarciaetal.2016,
  author    = {Shen, Yingjia and Chalopin, Domitille and Garcia, Tzintzuni and Boswell, Mikki and Boswell, William and Shiryev, Sergey A. and Agarwala, Richa and Volff, Jean-Nicolas and Postlethwait, John H. and Schartl, Manfred and Minx, Patrick and Warren, Wesley C. and Walter, Ronald B.},
  title     = {X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species},
  series = {BMC Genomics},
  volume    = {17},
  journal   = {BMC Genomics},
  doi       = {10.1186/s12864-015-2361-z},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-164582},
  pages     = {37},
  year      = {2016},
  abstract  = {Background Xiphophorus fishes are represented by 26 live-bearing species of tropical fish that express many attributes (e.g., viviparity, genetic and phenotypic variation, ecological adaptation, varied sexual developmental mechanisms, ability to produce fertile interspecies hybrids) that have made attractive research models for over 85 years. Use of various interspecies hybrids to investigate the genetics underlying spontaneous and induced tumorigenesis has resulted in the development and maintenance of pedigreed Xiphophorus lines specifically bred for research. The recent availability of the X. maculatus reference genome assembly now provides unprecedented opportunities for novel and exciting comparative research studies among Xiphophorus species. Results We present sequencing, assembly and annotation of two new genomes representing Xiphophorus couchianus and Xiphophorus hellerii. The final X. couchianus and X. hellerii assemblies have total sizes of 708 Mb and 734 Mb and correspond to 98 \% and 102 \% of the X. maculatus Jp 163 A genome size, respectively. The rates of single nucleotide change range from 1 per 52 bp to 1 per 69 bp among the three genomes and the impact of putatively damaging variants are presented. In addition, a survey of transposable elements allowed us to deduce an ancestral TE landscape, uncovered potential active TEs and document a recent burst of TEs during evolution of this genus. Conclusions Two new Xiphophorus genomes and their corresponding transcriptomes were efficiently assembled, the former using a novel guided assembly approach. Three assembled genome sequences within this single vertebrate order of new world live-bearing fishes will accelerate our understanding of relationship between environmental adaptation and genome evolution. In addition, these genome resources provide capability to determine allele specific gene regulation among interspecies hybrids produced by crossing any of the three species that are known to produce progeny predisposed to tumor development.},
  language  = {en}
}
@article{BrunetVolffSchartl2016,
  author    = {Brunet, Fr{\´e}d{\´e}ric G. and Volff, Jean-Nicolas and Schartl, Manfred},
  title     = {Whole Genome Duplications Shaped the Receptor Tyrosine Kinase Repertoire of Jawed Vertebrates},
  series = {Genome Biology Evolution},
  volume    = {8},
  journal   = {Genome Biology Evolution},
  number    = {15},
  doi       = {10.1093/gbe/evw103},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146988},
  pages     = {1600-1613},
  year      = {2016},
  abstract  = {The receptor tyrosine kinase (RTK) gene family, involved primarily in cell growth and differentiation, comprises proteins with a common enzymatic tyrosine kinase intracellular domain adjacent to a transmembrane region. The amino-terminal portion of RTKs is extracellular and made of different domains, the combination of which characterizes each of the 20 RTK subfamilies among mammals. We analyzed a total of 7,376 RTK sequences among 143 vertebrate species to provide here the first comprehensive census of the jawed vertebrate repertoire. We ascertained the 58 genes previously described in the human and mouse genomes and established their phylogenetic relationships. We also identified five additional RTKs amounting to a total of 63 genes in jawed vertebrates. We found that the vertebrate RTK gene family has been shaped by the two successive rounds of whole genome duplications (WGD) called 1R and 2R (1R/2R) that occurred at the base of the vertebrates. In addition, the Vegfr and Ephrin receptor subfamilies were expanded by single gene duplications. In teleost fish, 23 additional RTK genes have been retained after another expansion through the fish-specific third round (3R) of WGD. Several lineage-specific gene losses were observed. For instance, birds have lost three RTKs, and different genes are missing in several fish sublineages. The RTK gene family presents an unusual high gene retention rate from the vertebrate WGDs (58.75\% after 1R/2R, 64.4\% after 3R), resulting in an expansion that might be correlated with the evolution of complexity of vertebrate cellular communication and intracellular signaling.},
  language  = {en}
}
@article{BemmBeckerLarischetal.2016,
  author    = {Bemm, Felix and Becker, Dirk and Larisch, Christina and Kreuzer, Ines and Escalante-Perez, Maria and Schulze, Waltraud X. and Ankenbrand, Markus and Van de Weyer, Anna-Lena and Krol, Elzbieta and Al-Rasheid, Khaled A. and Mith{\"o}fer, Axel and Weber, Andreas P. and Schultz, J{\"o}rg and Hedrich, Rainer},
  title     = {Venus flytrap carnivorous lifestyle builds on herbivore defense strategies},
  series = {Genome Research},
  volume    = {26},
  journal   = {Genome Research},
  number    = {6},
  doi       = {10.1101/gr.202200.115},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-188799},
  pages     = {812-825},
  year      = {2016},
  abstract  = {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.},
  language  = {en}
}
@article{KaluzaWallaceHeardetal.2016,
  author    = {Kaluza, Benjamin F. and Wallace, Helen and Heard, Tim A. and Klein, Aelxandra-Maria and Leonhardt, Sara D.},
  title     = {Urban gardens promote bee foraging over natural habitats and plantations},
  series = {Ecology and Evolution},
  volume    = {6},
  journal   = {Ecology and Evolution},
  number    = {5},
  doi       = {10.1002/ece3.1941},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-162713},
  pages     = {1304-1316},
  year      = {2016},
  abstract  = {Increasing human land use for agriculture and housing leads to the loss of natural habitat and to widespread declines in wild bees. Bee foraging dynamics and fitness depend on the availability of resources in the surrounding landscape, but how precisely landscape related resource differences affect bee foraging patterns remains unclear. To investigate how landscape and its interaction with season and weather drive foraging and resource intake in social bees, we experimentally compared foraging activity, the allocation of foragers to different resources (pollen, nectar, and resin) and overall resource intake in the Australian stingless bee Tetragonula carbonaria (Apidae, Meliponini). Bee colonies were monitored in different seasons over two years. We compared foraging patterns and resource intake between the bees' natural habitat (forests) and two landscapes differently altered by humans (suburban gardens and agricultural macadamia plantations). We found foraging activity as well as pollen and nectar forager numbers to be highest in suburban gardens, intermediate in forests and low in plantations. Foraging patterns further differed between seasons, but seasonal variations strongly differed between landscapes. Sugar and pollen intake was low in plantations, but contrary with our predictions, it was even higher in gardens than in forests. In contrast, resin intake was similar across landscapes. Consequently, differences in resource availability between natural and altered landscapes strongly affect foraging patterns and thus resource intake in social bees. While agricultural monocultures largely reduce foraging success, suburban gardens can increase resource intake well above rates found in natural habitats of bees, indicating that human activities can both decrease and increase the availability of resources in a landscape and thus reduce or enhance bee fitness.},
  language  = {en}
}
@article{BenoitAdelmanReinhardtetal.2016,
  author    = {Benoit, Joshua B. and Adelman, Zach N. and Reinhardt, Klaus and Dolan, Amanda and Poelchau, Monica and Jennings, Emily C. and Szuter, Elise M. and Hagan, Richard W. and Gujar, Hemant and Shukla, Jayendra Nath and Zhu, Fang and Mohan, M. and Nelson, David R. and Rosendale, Andrew J. and Derst, Christian and Resnik, Valentina and Wernig, Sebastian and Menegazzi, Pamela and Wegener, Christian and Peschel, Nicolai and Hendershot, Jacob M. and Blenau, Wolfgang and Predel, Reinhard and Johnston, Paul R. and Ioannidis, Panagiotis and Waterhouse, Robert M. and Nauen, Ralf and Schorn, Corinna and Ott, Mark-Christoph and Maiwald, Frank and Johnston, J. Spencer and Gondhalekar, Ameya D. and Scharf, Michael E. and Raje, Kapil R. and Hottel, Benjamin A. and Armis{\´e}n, David and Crumi{\`e}re, Antonin Jean Johan and Refki, Peter Nagui and Santos, Maria Emilia and Sghaier, Essia and Viala, S{\`e}verine and Khila, Abderrahman and Ahn, Seung-Joon and Childers, Christopher and Lee, Chien-Yueh and Lin, Han and Hughes, Daniel S.T. and Duncan, Elizabeth J. and Murali, Shwetha C. and Qu, Jiaxin and Dugan, Shannon and Lee, Sandra L. and Chao, Hsu and Dinh, Huyen and Han, Yi and Doddapaneni, Harshavardhan and Worley, Kim C. and Muzny, Donna M. and Wheeler, David and Panfilio, Kristen A. and Jentzsch, Iris M. Vargas and Jentzsch, IMV and Vargo, Edward L. and Booth, Warren and Friedrich, Markus and Weirauch, Matthew T. and Anderson, Michelle A.E. and Jones, Jeffery W. and Mittapalli, Omprakash and Zhao, Chaoyang and Zhou, Jing-Jiang and Evans, Jay D. and Attardo, Geoffrey M. and Robertson, Hugh M. and Zdobnov, Evgeny M. and Ribeiro, Jose M.C. and Gibbs, Richard A. and Werren, John H. and Palli, Subba R. and Schal, Coby and Richards, Stephen},
  title     = {Unique features of a global human ectoparasite identified through sequencing of the bed bug genome},
  series = {Nature Communications},
  volume    = {7},
  journal   = {Nature Communications},
  number    = {10165},
  doi       = {10.1038/ncomms10165},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166221},
  year      = {2016},
  abstract  = {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.},
  language  = {en}
}
@article{daCruzRodriguezCasuriagaSantinaqueetal.2016,
  author    = {da Cruz, Irene and Rodr{\´i}guez-Casuriaga, Rosana and Santi{\~n}aque, Frederico F. and Far{\´i}as, Joaquina and Curti, Gianni and Capoano, Carlos A. and Folle, Gustavo A. and Benavente, Ricardo and Sotelo-Silveira, Jos{\´e} Roberto and Geisinger, Adriana},
  title     = {Transcriptome analysis of highly purified mouse spermatogenic cell populations: gene expression signatures switch from meiotic-to postmeiotic-related processes at pachytene stage},
  series = {BMC Genomics},
  volume    = {17},
  journal   = {BMC Genomics},
  doi       = {10.1186/s12864-016-2618-1},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-164574},
  pages     = {294},
  year      = {2016},
  abstract  = {Background Spermatogenesis is a complex differentiation process that involves the successive and simultaneous execution of three different gene expression programs: mitotic proliferation of spermatogonia, meiosis, and spermiogenesis. Testicular cell heterogeneity has hindered its molecular analyses. Moreover, the characterization of short, poorly represented cell stages such as initial meiotic prophase ones (leptotene and zygotene) has remained elusive, despite their crucial importance for understanding the fundamentals of meiosis. Results We have developed a flow cytometry-based approach for obtaining highly pure stage-specific spermatogenic cell populations, including early meiotic prophase. Here we combined this methodology with next generation sequencing, which enabled the analysis of meiotic and postmeiotic gene expression signatures in mouse with unprecedented reliability. Interestingly, we found that a considerable number of genes involved in early as well as late meiotic processes are already on at early meiotic prophase, with a high proportion of them being expressed only for the short time lapse of lepto-zygotene stages. Besides, we observed a massive change in gene expression patterns during medium meiotic prophase (pachytene) when mostly genes related to spermiogenesis and sperm function are already turned on. This indicates that the transcriptional switch from meiosis to post-meiosis takes place very early, during meiotic prophase, thus disclosing a higher incidence of post-transcriptional regulation in spermatogenesis than previously reported. Moreover, we found that a good proportion of the differential gene expression in spermiogenesis corresponds to up-regulation of genes whose expression starts earlier, at pachytene stage; this includes transition protein-and protamine-coding genes, which have long been claimed to switch on during spermiogenesis. In addition, our results afford new insights concerning X chromosome meiotic inactivation and reactivation. Conclusions This work provides for the first time an overview of the time course for the massive onset and turning off of the meiotic and spermiogenic genetic programs. Importantly, our data represent a highly reliable information set about gene expression in pure testicular cell populations including early meiotic prophase, for further data mining towards the elucidation of the molecular bases of male reproduction in mammals.},
  language  = {en}
}
@article{OthmanNaseemAwadetal.2016,
  author    = {Othman, Eman M. and Naseem, Muhammed and Awad, Eman and Dandekar, Thomas and Stopper, Helga},
  title     = {The Plant Hormone Cytokinin Confers Protection against Oxidative Stress in Mammalian Cells},
  series = {PLoS One},
  volume    = {11},
  journal   = {PLoS One},
  number    = {12},
  doi       = {10.1371/journal.pone.0168386},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147983},
  pages     = {e0168386},
  year      = {2016},
  abstract  = {Modulating key dynamics of plant growth and development, the effects of the plant hormone cytokinin on animal cells gained much attention recently. Most previous studies on cytokinin effects on mammalian cells have been conducted with elevated cytokinin concentration (in the μM range). However, to examine physiologically relevant dose effects of cytokinins on animal cells, we systematically analyzed the impact of kinetin in cultured cells at low and high concentrations (1nM-10μM) and examined cytotoxic and genotoxic conditions. We furthermore measured the intrinsic antioxidant activity of kinetin in a cell-free system using the Ferric Reducing Antioxidant Power assay and in cells using the dihydroethidium staining method. Monitoring viability, we looked at kinetin effects in mammalian cells such as HL60 cells, HaCaT human keratinocyte cells, NRK rat epithelial kidney cells and human peripheral lymphocytes. Kinetin manifests no antioxidant activity in the cell free system and high doses of kinetin (500 nM and higher) reduce cell viability and mediate DNA damage in vitro. In contrast, low doses (concentrations up to 100 nM) of kinetin confer protection in cells against oxidative stress. Moreover, our results show that pretreatment of the cells with kinetin significantly reduces 4-nitroquinoline 1-oxide mediated reactive oxygen species production. Also, pretreatment with kinetin retains cellular GSH levels when they are also treated with the GSH-depleting agent patulin. Our results explicitly show that low kinetin doses reduce apoptosis and protect cells from oxidative stress mediated cell death. Future studies on the interaction between cytokinins and human cellular pathway targets will be intriguing.},
  language  = {en}
}
@article{BiscottiGerdolCanapaetal.2016,
  author    = {Biscotti, Maria Assunta and Gerdol, Marco and Canapa, Adriana and Forconi, Mariko and Olmo, Ettore and Pallavicini, Alberto and Barucca, Marco and Schartl, Manfred},
  title     = {The Lungfish Transcriptome: A Glimpse into Molecular Evolution Events at the Transition from Water to Land},
  series = {Scientific Reports},
  volume    = {6},
  journal   = {Scientific Reports},
  number    = {21571},
  doi       = {10.1038/srep21571},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167753},
  year      = {2016},
  abstract  = {Lungfish and coelacanths are the only living sarcopterygian fish. The phylogenetic relationship of lungfish to the last common ancestor of tetrapods and their close morphological similarity to their fossil ancestors make this species uniquely interesting. However their genome size, the largest among vertebrates, is hampering the generation of a whole genome sequence. To provide a partial solution to the problem, a high-coverage lungfish reference transcriptome was generated and assembled. The present findings indicate that lungfish, not coelacanths, are the closest relatives to land-adapted vertebrates. Whereas protein-coding genes evolve at a very slow rate, possibly reflecting a "living fossil" status, transposable elements appear to be active and show high diversity, suggesting a role for them in the remarkable expansion of the lungfish genome. Analyses of single genes and gene families documented changes connected to the water to land transition and demonstrated the value of the lungfish reference transcriptome for comparative studies of vertebrate evolution.},
  language  = {en}
}
@article{KuenstnerHoffmannFraseretal.2016,
  author    = {K{\"u}nstner, Axel and Hoffmann, Margarete and Fraser, Bonnie A. and Kottler, Verena A. and Sharma, Eshita and Weigel, Detlef and Dreyer, Christine},
  title     = {The Genome of the Trinidadian Guppy, Poecilia reticulata, and Variation in the Guanapo Population},
  series = {PLoS ONE},
  volume    = {11},
  journal   = {PLoS ONE},
  number    = {12},
  doi       = {10.1371/journal.pone.0169087},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166755},
  pages     = {e0169087},
  year      = {2016},
  abstract  = {For over a century, the live bearing guppy, Poecilia reticulata, has been used to study sexual selection as well as local adaptation. Natural guppy populations differ in many traits that are of intuitively adaptive significance such as ornamentation, age at maturity, brood size and body shape. Water depth, light supply, food resources and predation regime shape these traits, and barrier waterfalls often separate contrasting environments in the same river. We have assembled and annotated the genome of an inbred single female from a high-predation site in the Guanapo drainage. The final assembly comprises 731.6 Mb with a scaffold N50 of 5.3 MB. Scaffolds were mapped to linkage groups, placing 95\% of the genome assembly on the 22 autosomes and the X-chromosome. To investigate genetic variation in the population used for the genome assembly, we sequenced 10 wild caught male individuals. The identified 5 million SNPs correspond to an average nucleotide diversity (π) of 0.0025. The genome assembly and SNP map provide a rich resource for investigating adaptation to different predation regimes. In addition, comparisons with the genomes of other Poeciliid species, which differ greatly in mechanisms of sex determination and maternal resource allocation, as well as comparisons to other teleost genera can begin to reveal how live bearing evolved in teleost fish.},
  language  = {en}
}
@article{ScharawIskarOrietal.2016,
  author    = {Scharaw, Sandra and Iskar, Murat and Ori, Alessandro and Boncompain, Gaelle and Laketa, Vibor and Poser, Ina and Lundberg, Emma and Perez, Franck and Beck, Martin and Bork, Peer and Pepperkok, Rainer},
  title     = {The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR},
  series = {Journal of Cell Biology},
  volume    = {215},
  journal   = {Journal of Cell Biology},
  number    = {4},
  doi       = {10.1083/jcb.201601090},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-186731},
  pages     = {543-558},
  year      = {2016},
  abstract  = {Stimulation of cells with epidermal growth factor (EGF) induces internalization and partial degradation of the EGF receptor (EGFR) by the endo-lysosomal pathway. For continuous cell functioning, EGFR plasma membrane levels are maintained by transporting newly synthesized EGFRs to the cell surface. The regulation of this process is largely unknown. In this study, we find that EGF stimulation specifically increases the transport efficiency of newly synthesized EGFRs from the endoplasmic reticulum to the plasma membrane. This coincides with an up-regulation of the inner coat protein complex II (COP II) components SEC23B, SEC24B, and SEC24D, which we show to be specifically required for EGFR transport. Up-regulation of these COP II components requires the transcriptional regulator RNF11, which localizes to early endosomes and appears additionally in the cell nucleus upon continuous EGF stimulation. Collectively, our work identifies a new regulatory mechanism that integrates the degradation and transport of EGFR in order to maintain its physiological levels at the plasma membrane.},
  language  = {en}
}
@article{KunzLiangNillaetal.2016,
  author    = {Kunz, Meik and Liang, Chunguang and Nilla, Santosh and Cecil, Alexander and Dandekar, Thomas},
  title     = {The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development},
  series = {Database},
  volume    = {2016},
  journal   = {Database},
  doi       = {10.1093/database/baw041},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147369},
  pages     = {baw041},
  year      = {2016},
  abstract  = {The drug-minded protein interaction database (DrumPID) has been designed to provide fast, tailored information on drugs and their protein networks including indications, protein targets and side-targets. Starting queries include compound, target and protein interactions and organism-specific protein families. Furthermore, drug name, chemical structures and their SMILES notation, affected proteins (potential drug targets), organisms as well as diseases can be queried including various combinations and refinement of searches. Drugs and protein interactions are analyzed in detail with reference to protein structures and catalytic domains, related compound structures as well as potential targets in other organisms. DrumPID considers drug functionality, compound similarity, target structure, interactome analysis and organismic range for a compound, useful for drug development, predicting drug side-effects and structure-activity relationships.},
  language  = {en}
}
@article{AnkenbrandWeberBeckeretal.2016,
  author    = {Ankenbrand, Markus J. and Weber, Lorenz and Becker, Dirk and F{\"o}rster, Frank and Bemm, Felix},
  title     = {TBro: visualization and management of de novo transcriptomes},
  series = {Database},
  volume    = {2016},
  journal   = {Database},
  doi       = {10.1093/database/baw146},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147954},
  pages     = {baw146},
  year      = {2016},
  abstract  = {RNA sequencing (RNA-seq) has become a powerful tool to understand molecular mechanisms and/or developmental programs. It provides a fast, reliable and cost-effective method to access sets of expressed elements in a qualitative and quantitative manner. Especially for non-model organisms and in absence of a reference genome, RNA-seq data is used to reconstruct and quantify transcriptomes at the same time. Even SNPs, InDels, and alternative splicing events are predicted directly from the data without having a reference genome at hand. A key challenge, especially for non-computational personnal, is the management of the resulting datasets, consisting of different data types and formats. Here, we present TBro, a flexible de novo transcriptome browser, tackling this challenge. TBro aggregates sequences, their annotation, expression levels as well as differential testing results. It provides an easy-to-use interface to mine the aggregated data and generate publication-ready visualizations. Additionally, it supports users with an intuitive cart system, that helps collecting and analysing biological meaningful sets of transcripts. TBro's modular architecture allows easy extension of its functionalities in the future. Especially, the integration of new data types such as proteomic quantifications or array-based gene expression data is straightforward. Thus, TBro is a fully featured yet flexible transcriptome browser that supports approaching complex biological questions and enhances collaboration of numerous researchers.},
  language  = {en}
}
@article{KaltdorfSrivastavaGuptaetal.2016,
  author    = {Kaltdorf, Martin and Srivastava, Mugdha and Gupta, Shishir K. and Liang, Chunguang and Binder, Jasmin and Dietl, Anna-Maria and Meir, Zohar and Haas, Hubertus and Osherov, Nir and Krappmann, Sven and Dandekar, Thomas},
  title     = {Systematic Identification of Anti-Fungal Drug Targets by a Metabolic Network Approach},
  series = {Frontiers in Molecular Bioscience},
  volume    = {3},
  journal   = {Frontiers in Molecular Bioscience},
  doi       = {10.3389/fmolb.2016.00022},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147396},
  pages     = {22},
  year      = {2016},
  abstract  = {New antimycotic drugs are challenging to find, as potential target proteins may have close human orthologs. We here focus on identifying metabolic targets that are critical for fungal growth and have minimal similarity to targets among human proteins. We compare and combine here: (I) direct metabolic network modeling using elementary mode analysis and flux estimates approximations using expression data, (II) targeting metabolic genes by transcriptome analysis of condition-specific highly expressed enzymes, and (III) analysis of enzyme structure, enzyme interconnectedness ("hubs"), and identification of pathogen-specific enzymes using orthology relations. We have identified 64 targets including metabolic enzymes involved in vitamin synthesis, lipid, and amino acid biosynthesis including 18 targets validated from the literature, two validated and five currently examined in own genetic experiments, and 38 further promising novel target proteins which are non-orthologous to human proteins, involved in metabolism and are highly ranked drug targets from these pipelines.},
  language  = {en}
}
@article{GattoSchulzeNielsen2016,
  author    = {Gatto, Francesco and Schulze, Almut and Nielsen, Jens},
  title     = {Systematic Analysis Reveals that Cancer Mutations Converge on Deregulated Metabolism of Arachidonate and Xenobiotics},
  series = {Cell Reports},
  volume    = {16},
  journal   = {Cell Reports},
  number    = {3},
  doi       = {10.1016/j.celrep.2016.06.038},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-164814},
  pages     = {878-895},
  year      = {2016},
  abstract  = {Mutations are the basis of the clonal evolution of most cancers. Nevertheless, a systematic analysis of whether mutations are selected in cancer because they lead to the deregulation of specific biological processes independent of the type of cancer is still lacking. In this study, we correlated the genome and transcriptome of 1,082 tumors. We found that nine commonly mutated genes correlated with substantial changes in gene expression, which primarily converged on metabolism. Further network analyses circumscribed the convergence to a network of reactions, termed AraX, that involves the glutathione- and oxygen-mediated metabolism of arachidonic acid and xenobiotics. In an independent cohort of 4,462 samples, all nine mutated genes were consistently correlated with the deregulation of AraX. Among all of the metabolic pathways, AraX deregulation represented the strongest predictor of patient survival. These findings suggest that oncogenic mutations drive a selection process that converges on the deregulation of the AraX network.},
  language  = {en}
}
@article{GrimmKleinKopeketal.2016,
  author    = {Grimm, Jonathan B. and Klein, Teresa and Kopek, Benjamin G. and Shtengel, Gleb and Hess, Harald F. and Sauer, Markus and Lavis, Luke D.},
  title     = {Synthesis of a far-red photoactivatable silicon-containing rhodamine for super-resolution microscopy},
  series = {Angewandte Chemie International Edition},
  volume    = {55},
  journal   = {Angewandte Chemie International Edition},
  number    = {5},
  doi       = {10.1002/anie.201509649},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-191069},
  pages     = {1723-1727},
  year      = {2016},
  abstract  = {The rhodamine system is a flexible framework for building small-molecule fluorescent probes. Changing N-substitution patterns and replacing the xanthene oxygen with a dimethylsilicon moiety can shift the absorption and fluorescence emission maxima of rhodamine dyes to longer wavelengths. Acylation of the rhodamine nitrogen atoms forces the molecule to adopt a nonfluorescent lactone form, providing a convenient method to make fluorogenic compounds. Herein, we take advantage of all of these structural manipulations and describe a novel photoactivatable fluorophore based on a Si-containing analogue of Q-rhodamine. This probe is the first example of a "caged" Si-rhodamine, exhibits higher photon counts compared to established localization microscopy dyes, and is sufficiently red-shifted to allow multicolor imaging. The dye is a useful label for super-resolution imaging and constitutes a new scaffold for far-red fluorogenic molecules.},
  language  = {en}
}
@article{MenaDiegelmannWegeneretal.2016,
  author    = {Mena, Wilson and Diegelmann, S{\"o}ren and Wegener, Christian and Ewer, John},
  title     = {Stereotyped responses of Drosophila peptidergic neuronal ensemble depend on downstream neuromodulators},
  series = {eLife},
  volume    = {5},
  journal   = {eLife},
  doi       = {10.7554/eLife.19686},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-165003},
  pages     = {e19686},
  year      = {2016},
  abstract  = {Neuropeptides play a key role in the regulation of behaviors and physiological responses including alertness, social recognition, and hunger, yet, their mechanism of action is poorly understood. Here, we focus on the endocrine control ecdysis behavior, which is used by arthropods to shed their cuticle at the end of every molt. Ecdysis is triggered by ETH (Ecdysis triggering hormone), and we show that the response of peptidergic neurons that produce CCAP (crustacean cardioactive peptide), which are key targets of ETH and control the onset of ecdysis behavior, depends fundamentally on the actions of neuropeptides produced by other direct targets of ETH and released in a broad paracrine manner within the CNS; by autocrine influences from the CCAP neurons themselves; and by inhibitory actions mediated by GABA. Our findings provide insights into how this critical insect behavior is controlled and general principles for understanding how neuropeptides organize neuronal activity and behaviors.},
  language  = {en}
}
@article{BlaettnerDasPaprotkaetal.2016,
  author    = {Bl{\"a}ttner, Sebastian and Das, Sudip and Paprotka, Kerstin and Eilers, Ursula and Krischke, Markus and Kretschmer, Dorothee and Remmele, Christian W. and Dittrich, Marcus and M{\"u}ller, Tobias and Schuelein-Voelk, Christina and Hertlein, Tobias and Mueller, Martin J. and Huettel, Bruno and Reinhardt, Richard and Ohlsen, Knut and Rudel, Thomas and Fraunholz, Martin J.},
  title     = {Staphylococcus aureus Exploits a Non-ribosomal Cyclic Dipeptide to Modulate Survival within Epithelial Cells and Phagocytes},
  series = {PLoS Pathogens},
  volume    = {12},
  journal   = {PLoS Pathogens},
  number    = {9},
  doi       = {10.1371/journal.ppat.1005857},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-180380},
  year      = {2016},
  abstract  = {Community-acquired (CA) Staphylococcus aureus cause various diseases even in healthy individuals. Enhanced virulence of CA-strains is partly attributed to increased production of toxins such as phenol-soluble modulins (PSM). The pathogen is internalized efficiently by mammalian host cells and intracellular S. aureus has recently been shown to contribute to disease. Upon internalization, cytotoxic S. aureus strains can disrupt phagosomal membranes and kill host cells in a PSM-dependent manner. However, PSM are not sufficient for these processes. Here we screened for factors required for intracellular S. aureus virulence. We infected escape reporter host cells with strains from an established transposon mutant library and detected phagosomal escape rates using automated microscopy. We thereby, among other factors, identified a non-ribosomal peptide synthetase (NRPS) to be required for efficient phagosomal escape and intracellular survival of S. aureus as well as induction of host cell death. By genetic complementation as well as supplementation with the synthetic NRPS product, the cyclic dipeptide phevalin, wild-type phenotypes were restored. We further demonstrate that the NRPS is contributing to virulence in a mouse pneumonia model. Together, our data illustrate a hitherto unrecognized function of the S. aureus NRPS and its dipeptide product during S. aureus infection.},
  language  = {en}
}
@article{BargulJungMcOdimbaetal.2016,
  author    = {Bargul, Joel L. and Jung, Jamin and McOdimba, Francis A. and Omogo, Collins O. and Adung'a, Vincent O. and Kr{\"u}ger, Timothy and Masiga, Daniel K. and Engstler, Markus},
  title     = {Species-Specific Adaptations of Trypanosome Morphology and Motility to the Mammalian Host},
  series = {PLoS Pathogens},
  volume    = {12},
  journal   = {PLoS Pathogens},
  number    = {2},
  doi       = {10.1371/journal.ppat.1005448},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146513},
  pages     = {e1005448},
  year      = {2016},
  abstract  = {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.},
  language  = {en}
}
@article{Kramer2016,
  author    = {Kramer, Susanne},
  title     = {Simultaneous detection of mRNA transcription and decay intermediates by dual colour single mRNA FISH on subcellular resolution},
  series = {Nucleic Acids Research},
  journal   = {Nucleic Acids Research},
  doi       = {10.1093/nar/gkw1245},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-148002},
  pages     = {gkw1245},
  year      = {2016},
  abstract  = {The detection of mRNAs undergoing transcription or decay is challenging, because both processes are fast. However, the relative proportion of an mRNA in synthesis or decay increases with mRNA size and decreases with mRNA half-life. Based on this rationale, I have exploited a 22 200 nucleotide-long, short-lived endogenous mRNA as a reporter for mRNA metabolism in trypanosomes. The extreme 5΄ and 3΄ ends were labeled with red- and green-fluorescent Affymetrix® single mRNA FISH probes, respectively. In the resulting fluorescence images, yellow spots represent intact mRNAs; red spots are mRNAs in transcription or 3΄-5΄ decay, and green spots are mRNAs in 5΄-3΄ degradation. Most red spots were nuclear and insensitive to transcriptional inhibition and thus likely transcription intermediates. Most green spots were cytoplasmic, confirming that the majority of cytoplasmic decay in trypanosomes is 5΄-3΄. The system showed the expected changes at inhibition of transcription or translation and RNAi depletion of the trypanosome homologue to the 5΄-3΄ exoribonuclease Xrn1. The method allows to monitor changes in mRNA metabolism both on cellular and on population/tissue wide levels, but also to study the subcellular localization of mRNA transcription and decay pathways. I show that the system is applicable to mammalian cells.},
  language  = {en}
}
@article{JahnMarkertRyuetal.2016,
  author    = {Jahn, Martin T. and Markert, Sebastian M. and Ryu, Taewoo and Ravasi, Timothy and Stigloher, Christian and Hentschel, Ute and Moitinho-Silva, Lucas},
  title     = {Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling},
  series = {Scientific Reports},
  volume    = {6},
  journal   = {Scientific Reports},
  number    = {35860},
  doi       = {10.1038/srep35860},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167513},
  year      = {2016},
  abstract  = {Assigning functions to uncultivated environmental microorganisms continues to be a challenging endeavour. Here, we present a new microscopy protocol for fluorescence in situ hybridisation-correlative light and electron microscopy (FISH-CLEM) that enabled, to our knowledge for the first time, the identification of single cells within their complex microenvironment at electron microscopy resolution. Members of the candidate phylum Poribacteria, common and uncultivated symbionts of marine sponges, were used towards this goal. Cellular 3D reconstructions revealed bipolar, spherical granules of low electron density, which likely represent carbon reserves. Poribacterial activity profiles were retrieved from prokaryotic enriched sponge metatranscriptomes using simulation-based optimised mapping. We observed high transcriptional activity for proteins related to bacterial microcompartments (BMC) and we resolved their subcellular localisation by combining FISH-CLEM with immunohistochemistry (IHC) on ultra-thin sponge tissue sections. In terms of functional relevance, we propose that the BMC-A region may be involved in 1,2-propanediol degradation. The FISH-IHC-CLEM approach was proven an effective toolkit to combine -omics approaches with functional studies and it should be widely applicable in environmental microbiology.},
  language  = {en}
}
@article{SinghVermaAkhoonetal.2016,
  author    = {Singh, Krishna P. and Verma, Neeraj and Akhoon, Bashir A . and Bhatt, Vishal and Gupta, Shishir K. and Gupta, Shailendra K. and Smita, Suchi},
  title     = {Sequence-based approach for rapid identification of cross-clade CD8+ T-cell vaccine candidates from all high-risk HPV strains},
  series = {3 Biotech},
  volume    = {6},
  journal   = {3 Biotech},
  doi       = {10.1007/s13205-015-0352-z},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-191056},
  pages     = {10},
  year      = {2016},
  abstract  = {Human papilloma virus (HPV) is the primary etiological agent responsible for cervical cancer in women. Although in total 16 high-risk HPV strains have been identified so far. Currently available commercial vaccines are designed by targeting mainly HPV16 and HPV18 viral strains as these are the most common strains associated with cervical cancer. Because of the high level of antigenic specificity of HPV capsid antigens, the currently available vaccines are not suitable to provide cross-protection from all other high-risk HPV strains. Due to increasing reports of cervical cancer cases from other HPV high-risk strains other than HPV16 and 18, it is crucial to design vaccine that generate reasonable CD8+ T-cell responses for possibly all the high-risk strains. With this aim, we have developed a computational workflow to identify conserved cross-clade CD8+ T-cell HPV vaccine candidates by considering E1, E2, E6 and E7 proteins from all the high-risk HPV strains. We have identified a set of 14 immunogenic conserved peptide fragments that are supposed to provide protection against infection from any of the high-risk HPV strains across globe.},
  language  = {en}
}
@article{HeurichZeisKuechenhoffetal.2016,
  author    = {Heurich, Marco and Zeis, Klara and K{\"u}chenhoff, Helmut and M{\"u}ller, J{\"o}rg and Belotti, Elisa and Bufka, Luděk and Woelfing, Benno},
  title     = {Selective Predation of a Stalking Predator on Ungulate Prey},
  series = {PLoS ONE},
  volume    = {11},
  journal   = {PLoS ONE},
  number    = {8},
  doi       = {10.1371/journal.pone.0158449},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166827},
  pages     = {e0158449},
  year      = {2016},
  abstract  = {Prey selection is a key factor shaping animal populations and evolutionary dynamics. An optimal forager should target prey that offers the highest benefits in terms of energy content at the lowest costs. Predators are therefore expected to select for prey of optimal size. Stalking predators do not pursue their prey long, which may lead to a more random choice of prey individuals. Due to difficulties in assessing the composition of available prey populations, data on prey selection of stalking carnivores are still scarce. We show how the stalking predator Eurasian lynx (Lynx lynx) selects prey individuals based on species identity, age, sex and individual behaviour. To address the difficulties in assessing prey population structure, we confirm inferred selection patterns by using two independent data sets: (1) data of 387 documented kills of radio-collared lynx were compared to the prey population structure retrieved from systematic camera trapping using Manly's standardized selection ratio alpha and (2) data on 120 radio-collared roe deer were analysed using a Cox proportional hazards model. Among the larger red deer prey, lynx selected against adult males—the largest and potentially most dangerous prey individuals. In roe deer lynx preyed selectively on males and did not select for a specific age class. Activity during high risk periods reduced the risk of falling victim to a lynx attack. Our results suggest that the stalking predator lynx actively selects for size, while prey behaviour induces selection by encounter and stalking success rates.},
  language  = {en}
}
@article{SenthilanHelfrichFoerster2016,
  author    = {Senthilan, Pingkalai R. and Helfrich-F{\"o}rster, Charlotte},
  title     = {Rhodopsin 7-The unusual Rhodopsin in Drosophila},
  series = {PeerJ},
  volume    = {4},
  journal   = {PeerJ},
  doi       = {10.7717/peerj.2427},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-177998},
  year      = {2016},
  abstract  = {Rhodopsins are the major photopigments in the fruit fly Drosophila melanogaster. Drosophila express six well-characterized Rhodopsins (Rh1-Rh6) with distinct absorption maxima and expression pattern. In 2000, when the Drosophila genome was published, a novel Rhodopsin gene was discovered: Rhodopsin 7 (Rh7). Rh7 is highly conserved among the Drosophila genus and is also found in other arthropods. Phylogenetic trees based on protein sequences suggest that the seven Drosophila Rhodopsins cluster in three different groups. While Rh1, Rh2 and Rh6 form a "vertebrate-melanopsin-type"-cluster, and Rh3, Rh4 and Rh5 form an "insect-type"-Rhodopsin cluster, Rh7 seem to form its own cluster. Although Rh7 has nearly all important features of a functional Rhodopsin, it differs from other Rhodopsins in its genomic and structural properties, suggesting it might have an overall different role than other known Rhodopsins.},
  language  = {en}
}
@article{HassounaOttWuestefeldetal.2016,
  author    = {Hassouna, I. and Ott, C. and W{\"u}stefeld, L. and Offen, N. and Neher, R. A. and Mitkovski, M. and Winkler, D. and Sperling, S. and Fries, L. and Goebbels, S. and Vreja, I. C. and Hagemeyer, N. and Dittrich, M. and Rossetti, M. F. and Kr{\"o}hnert, K. and Hannke, K. and Boretius, S. and Zeug, A. and H{\"o}schen, C. and Dandekar, T. and Dere, E. and Neher, E. and Rizzoli, S. O. and Nave, K.-A. and Sir{\´e}n, A.-L. and Ehrenreich, H.},
  title     = {Revisiting adult neurogenesis and the role of erythropoietin for neuronal and oligodendroglial differentiation in the hippocampus},
  series = {Molecular Psychiatry},
  volume    = {21},
  journal   = {Molecular Psychiatry},
  number    = {12},
  doi       = {10.1038/mp.2015.212},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-186669},
  pages     = {1752-1767},
  year      = {2016},
  abstract  = {Recombinant human erythropoietin (EPO) improves cognitive performance in neuropsychiatric diseases ranging from schizophrenia and multiple sclerosis to major depression and bipolar disease. This consistent EPO effect on cognition is independent of its role in hematopoiesis. The cellular mechanisms of action in brain, however, have remained unclear. Here we studied healthy young mice and observed that 3-week EPO administration was associated with an increased number of pyramidal neurons and oligodendrocytes in the hippocampus of similar to 20\%. Under constant cognitive challenge, neuron numbers remained elevated until >6 months of age. Surprisingly, this increase occurred in absence of altered cell proliferation or apoptosis. After feeding a \(^{15}\)N-leucine diet, we used nanoscopic secondary ion mass spectrometry, and found that in EPO-treated mice, an equivalent number of neurons was defined by elevated \(^{15}\)N-leucine incorporation. In EPO-treated NG2-Cre-ERT2 mice, we confirmed enhanced differentiation of preexisting oligodendrocyte precursors in the absence of elevated DNA synthesis. A corresponding analysis of the neuronal lineage awaits the identification of suitable neuronal markers. In cultured neurospheres, EPO reduced Sox9 and stimulated miR124, associated with advanced neuronal differentiation. We are discussing a resulting working model in which EPO drives the differentiation of non-dividing precursors in both (NG2+) oligodendroglial and neuronal lineages. As endogenous EPO expression is induced by brain injury, such a mechanism of adult neurogenesis may be relevant for central nervous system regeneration.},
  language  = {en}
}
@article{AdolfiHerpinRegensburgeretal.2016,
  author    = {Adolfi, Mateus C. and Herpin, Amaury and Regensburger, Martina and Sacquegno, Jacopo and Waxman, Joshua S. and Schartl, Manfred},
  title     = {Retinoic acid and meiosis induction in adult versus embryonic gonads of medaka},
  series = {Scientific Reports},
  volume    = {6},
  journal   = {Scientific Reports},
  doi       = {10.1038/srep34281},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147843},
  pages     = {34281},
  year      = {2016},
  abstract  = {In vertebrates, one of the first recognizable sex differences in embryos is the onset of meiosis, known to be regulated by retinoic acid (RA) in mammals. We investigated in medaka a possible meiotic function of RA during the embryonic sex determination (SD) period and in mature gonads. We found RA mediated transcriptional activation in germ cells of both sexes much earlier than the SD stage, however, no such activity during the critical stages of SD. In adults, expression of the RA metabolizing enzymes indicates sexually dimorphic RA levels. In testis, RA acts directly in Sertoli, Leydig and pre-meiotic germ cells. In ovaries, RA transcriptional activity is highest in meiotic oocytes. Our results show that RA plays an important role in meiosis induction and gametogenesis in adult medaka but contrary to common expectations, not for initiating the first meiosis in female germ cells at the SD stage.},
  language  = {en}
}
@article{EndresKneitzOrthetal.2016,
  author    = {Endres, Marcel and Kneitz, Susanne and Orth, Martin F. and Perera, Ruwan K. and Zernecke, Alma and Butt, Elke},
  title     = {Regulation of matrix metalloproteinases (MMPs) expression and secretion in MDA-MB-231 breast cancer cells by LIM and SH3 protein 1 (LASP1)},
  series = {Oncotarget},
  volume    = {7},
  journal   = {Oncotarget},
  number    = {39},
  doi       = {10.18632/oncotarget.11720},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-176920},
  pages     = {64244-64259},
  year      = {2016},
  abstract  = {The process of tumor invasion requires degradation of extracellular matrix by proteolytic enzymes. Cancer cells form protrusive invadopodia, which produce and release matrix metalloproteinases (MMPs) to degrade the basement membrane thereby enabling metastasis. We investigated the effect of LASP1, a newly identified protein in invadopodia, on expression, secretion and activation of MMPs in invasive breast tumor cell lines. By analyzing microarray data of in-house generated control and LASP1-depleted MDA-MB-231 breast cancer cells, we observed downregulation of MMP1, -3 and -9 upon LASP1 depletion. This was confirmed by Western blot analysis. Conversely, rescue experiments restored in part MMP expression and secretion. The regulatory effect of LASP1 on MMP expression was also observed in BT-20 breast cancer cells as well as in prostate and bladder cancer cell lines. In line with bioinformatic FunRich analysis of our data, which mapped a high regulation of transcription factors by LASP1, public microarray data analysis detected a correlation between high LASP1 expression and enhanced c-Fos levels, a protein that is part of the transcription factor AP-1 and known to regulate MMP expression. Compatibly, in luciferase reporter assays, AP-1 showed a decreased transcriptional activity after LASP1 knockdown. Zymography assays and Western blot analysis revealed an additional promotion of MMP secretion into the extracellular matrix by LASP1, thus, most likely, altering the microenvironment during cancer progression. The newly identified role of LASP1 in regulating matrix degradation by affecting MMP transcription and secretion elucidated the migratory potential of LASP1 overexpressing aggressive tumor cells in earlier studies.},
  language  = {en}
}
@article{DreschersSauppHornefetal.2016,
  author    = {Dreschers, Stephan and Saupp, Peter and Hornef, Mathias and Prehn, Andrea and Platen, Christopher and Morschh{\"a}user, Joachim and Orlikowsky, Thorsten W.},
  title     = {Reduced PICD in Monocytes Mounts Altered Neonate Immune Response to Candida albicans},
  series = {PLoS ONE},
  volume    = {11},
  journal   = {PLoS ONE},
  number    = {11},
  doi       = {10.1371/journal.pone.0166648},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166778},
  pages     = {e0166648},
  year      = {2016},
  abstract  = {Background Invasive fungal infections with Candida albicans (C. albicans) occur frequently in extremely low birthweight (ELBW) infants and are associated with poor outcome. Phagocytosis of C.albicans initializes apoptosis in monocytes (phagocytosis induced cell death, PICD). PICD is reduced in neonatal cord blood monocytes (CBMO). Hypothesis Phagocytosis of C. albicans causes PICD which differs between neonatal monocytes (CBMO) and adult peripheral blood monocytes (PBMO) due to lower stimulation of TLR-mediated immune responses. Methods The ability to phagocytose C. albicans, expression of TLRs, the induction of apoptosis (assessment of sub-G1 and nick-strand breaks) were analyzed by FACS. TLR signalling was induced by agonists such as lipopolysaccharide (LPS), Pam3Cys, FSL-1 and Zymosan and blocked (neutralizing TLR2 antibodies and MYD88 inhibitor). Results Phagocytic indices of PBMO and CBMO were similar. Following stimulation with agonists and C. albicans induced up-regulation of TLR2 and consecutive phosphorylation of MAP kinase P38 and expression of TNF-α, which were stronger on PBMO compared to CBMO (p < 0.005). Downstream, TLR2 signalling initiated caspase-3-dependent PICD which was found reduced in CBMO (p < 0.05 vs PBMO). Conclusion Our data suggest direct involvement of TLR2-signalling in C. albicans-induced PICD in monocytes and an alteration of this pathway in CBMO.},
  language  = {en}
}
@article{KonteTerpitzPlemenitaš2016,
  author    = {Konte, Tilen and Terpitz, Ulrich and Plemenitaš, Ana},
  title     = {Reconstruction of the High-Osmolarity Glycerol (HOG) Signaling Pathway from the Halophilic Fungus Wallemia ichthyophaga in Saccharomyces cerevisiae},
  series = {Frontiers in Microbiology},
  journal   = {Frontiers in Microbiology},
  doi       = {10.3389/fmicb.2016.00901},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-165214},
  year      = {2016},
  abstract  = {The basidiomycetous fungus Wallemia ichthyophaga grows between 1.7 and 5.1 M NaCl and is the most halophilic eukaryote described to date. Like other fungi, W. ichthyophaga detects changes in environmental salinity mainly by the evolutionarily conserved high-osmolarity glycerol (HOG) signaling pathway. In Saccharomyces cerevisiae, the HOG pathway has been extensively studied in connection to osmotic regulation, with a valuable knock-out strain collection established. In the present study, we reconstructed the architecture of the HOG pathway of W. ichthyophaga in suitable S. cerevisiae knock-out strains, through heterologous expression of the W. ichthyophaga HOG pathway proteins. Compared to S. cerevisiae, where the Pbs2 (ScPbs2) kinase of the HOG pathway is activated via the SHO1 and SLN1 branches, the interactions between the W. ichthyophaga Pbs2 (WiPbs2) kinase and the W. ichthyophaga SHO1 branch orthologs are not conserved: as well as evidence of poor interactions between the WiSho1 Src-homology 3 (SH3) domain and the WiPbs2 proline-rich motif, the absence of a considerable part of the osmosensing apparatus in the genome of W. ichthyophaga suggests that the SHO1 branch components are not involved in HOG signaling in this halophilic fungus. In contrast, the conserved activation of WiPbs2 by the S. cerevisiae ScSsk2/ScSsk22 kinase and the sensitivity of W. ichthyophaga cells to fludioxonil, emphasize the significance of two-component (SLN1-like) signaling via Group III histidine kinase. Combined with protein modeling data, our study reveals conserved and non-conserved protein interactions in the HOG signaling pathway of W. ichthyophaga and therefore significantly improves the knowledge of hyperosmotic signal processing in this halophilic fungus.},
  language  = {en}
}
@article{Hoelldobler2016,
  author    = {H{\"o}lldobler, Bert},
  title     = {Queen Specific Exocrine Glands in Legionary Ants and Their Possible Function in Sexual Selection},
  series = {PLoS ONE},
  volume    = {11},
  journal   = {PLoS ONE},
  number    = {3},
  doi       = {10.1371/journal.pone.0151604},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167057},
  pages     = {e0151604},
  year      = {2016},
  abstract  = {The colonies of army ants and some other legionary ant species have single, permanently wingless queens with massive post petioles and large gasters. Such highly modified queens are called dichthadiigynes. This paper presents the unusually rich exocrine gland endowment of dichthadiigynes, which is not found in queens of other ant species. It has been suggested these kinds of glands produce secretions that attract and maintain worker retinues around queens, especially during migration. However, large worker retinues also occur in non-legionary species whose queens do not have such an exuberance of exocrine glands. We argue and present evidence in support of our previously proposed hypothesis that the enormous outfit of exocrine glands found in dichthadiigynes is due to sexual selection mediated by workers as the main selecting agents},
  language  = {en}
}
@article{DiaoMoussetHorsburghetal.2016,
  author    = {Diao, Wenwen and Mousset, Mathilde and Horsburgh, Gavin J. and Vermeulen, Cornelis J. and Johannes, Frank and van de Zande, Louis and Ritchie, Michael G. and Schmitt, Thomas and Beukeboom, Leo W.},
  title     = {Quantitative Trait Locus Analysis of Mating Behavior and Male Sex Pheromones in Nasonia Wasps},
  series = {G3: Genes Genomes Genetics},
  volume    = {6},
  journal   = {G3: Genes Genomes Genetics},
  number    = {6},
  doi       = {10.1534/g3.116.029074},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-165412},
  pages     = {1549-1562},
  year      = {2016},
  abstract  = {A major focus in speciation genetics is to identify the chromosomal regions and genes that reduce hybridization and gene flow. We investigated the genetic architecture of mating behavior in the parasitoid wasp species pair Nasonia giraulti and Nasonia oneida that exhibit strong prezygotic isolation. Behavioral analysis showed that N. oneida females had consistently higher latency times, and broke off the mating sequence more often in the mounting stage when confronted with N. giraulti males compared with males of their own species. N. oneida males produce a lower quantity of the long-range male sex pheromone (4R,5S)-5-hydroxy-4-decanolide (RS-HDL). Crosses between the two species yielded hybrid males with various pheromone quantities, and these males were used in mating trials with females of either species to measure female mate discrimination rates. A quantitative trait locus (QTL) analysis involving 475 recombinant hybrid males (F2), 2148 reciprocally backcrossed females (F3), and a linkage map of 52 equally spaced neutral single nucleotide polymorphism (SNP) markers plus SNPs in 40 candidate mating behavior genes revealed four QTL for male pheromone amount, depending on partner species. Our results demonstrate that the RS-HDL pheromone plays a role in the mating system of N. giraulti and N. oneida, but also that additional communication cues are involved in mate choice. No QTL were found for female mate discrimination, which points at a polygenic architecture of female choice with strong environmental influences.},
  language  = {en}
}
@article{DejungSubotaBuceriusetal.2016,
  author    = {Dejung, Mario and Subota, Ines and Bucerius, Ferdinand and Dindar, G{\"u}lcin and Freiwald, Anja and Engstler, Markus and Boshart, Michael and Butter, Falk and Janzen, Chistian J.},
  title     = {Quantitative proteomics uncovers novel factors involved in developmental differentiation of Trypanosoma brucei},
  series = {PLoS Pathogens},
  volume    = {12},
  journal   = {PLoS Pathogens},
  number    = {2},
  doi       = {10.1371/journal.ppat.1005439},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146362},
  pages     = {e1005439},
  year      = {2016},
  abstract  = {Developmental differentiation is a universal biological process that allows cells to adapt to different environments to perform specific functions. African trypanosomes progress through a tightly regulated life cycle in order to survive in different host environments when they shuttle between an insect vector and a vertebrate host. Transcriptomics has been useful to gain insight into RNA changes during stage transitions; however, RNA levels are only a moderate proxy for protein abundance in trypanosomes. We quantified 4270 protein groups during stage differentiation from the mammalian-infective to the insect form and provide classification for their expression profiles during development. Our label-free quantitative proteomics study revealed previously unknown components of the differentiation machinery that are involved in essential biological processes such as signaling, posttranslational protein modifications, trafficking and nuclear transport. Furthermore, guided by our proteomic survey, we identified the cause of the previously observed differentiation impairment in the histone methyltransferase DOT1B knock-out strain as it is required for accurate karyokinesis in the first cell division during differentiation. This epigenetic regulator is likely involved in essential chromatin restructuring during developmental differentiation, which might also be important for differentiation in higher eukaryotic cells. Our proteome dataset will serve as a resource for detailed investigations of cell differentiation to shed more light on the molecular mechanisms of this process in trypanosomes and other eukaryotes.},
  language  = {en}
}
@article{VendelovadeLimaLorenzattoetal.2016,
  author    = {Vendelova, Emilia and de Lima, Jeferson Camargo and Lorenzatto, Karina Rodrigues and Monteiro, Karina Mariante and Mueller, Thomas and Veepaschit, Jyotishman and Grimm, Clemens and Brehm, Klaus and Hrčkov{\´a}, Gabriela and Lutz, Manfred B. and Ferreira, Henrique B. and Nono, Justin Komguep},
  title     = {Proteomic Analysis of Excretory-Secretory Products of Mesocestoides corti Metacestodes Reveals Potential Suppressors of Dendritic Cell Functions},
  series = {PLoS Neglected Tropical Diseases},
  volume    = {10},
  journal   = {PLoS Neglected Tropical Diseases},
  number    = {10},
  doi       = {10.1371/journal.pntd.0005061},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166742},
  pages     = {e0005061},
  year      = {2016},
  abstract  = {Accumulating evidences have assigned a central role to parasite-derived proteins in immunomodulation. Here, we report on the proteomic identification and characterization of immunomodulatory excretory-secretory (ES) products from the metacestode larva (tetrathyridium) of the tapeworm Mesocestoides corti (syn. M. vogae). We demonstrate that ES products but not larval homogenates inhibit the stimuli-driven release of the pro-inflammatory, Th1-inducing cytokine IL-12p70 by murine bone marrow-derived dendritic cells (BMDCs). Within the ES fraction, we biochemically narrowed down the immunosuppressive activity to glycoproteins since active components were lipid-free, but sensitive to heat- and carbohydrate-treatment. Finally, using bioassay-guided chromatographic analyses assisted by comparative proteomics of active and inactive fractions of the ES products, we defined a comprehensive list of candidate proteins released by M. corti tetrathyridia as potential suppressors of DC functions. Our study provides a comprehensive library of somatic and ES products and highlight some candidate parasite factors that might drive the subversion of DC functions to facilitate the persistence of M. corti tetrathyridia in their hosts.},
  language  = {en}
}
@article{PetersHempAppelhansetal.2016,
  author    = {Peters, Marcell K. and Hemp, Andreas and Appelhans, Tim and Behler, Christina and Classen, Alice and Detsch, Florian and Ensslin, Andreas and Ferger, Stefan W. and Frederiksen, Sara B. and Gebert, Frederike and Haas, Michael and Helbig-Bonitz, Maria and Hemp, Claudia and Kindeketa, William J. and Mwangomo, Ephraim and Ngereza, Christine and Otte, Insa and R{\"o}der, Juliane and Rutten, Gemma and Costa, David Schellenberger and Tardanico, Joseph and Zancolli, Giulia and Deckert, J{\"u}rgen and Eardley, Connal D. and Peters, Ralph S. and R{\"o}del, Mark-Oliver and Schleuning, Matthias and Ssymank, Axel and Kakengi, Victor and Zhang, Jie and B{\"o}hning-Gaese, Katrin and Brandl, Roland and Kalko, Elisabeth K.V. and Kleyer, Michael and Nauss, Thomas and Tschapka, Marco and Fischer, Markus and Steffan-Dewenter, Ingolf},
  title     = {Predictors of elevational biodiversity gradients change from single taxa to the multi-taxa community level},
  series = {Nature Communications},
  volume    = {7},
  journal   = {Nature Communications},
  doi       = {10.1038/ncomms13736},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-169374},
  year      = {2016},
  abstract  = {The factors determining gradients of biodiversity are a fundamental yet unresolved topic in ecology. While diversity gradients have been analysed for numerous single taxa, progress towards general explanatory models has been hampered by limitations in the phylogenetic coverage of past studies. By parallel sampling of 25 major plant and animal taxa along a 3.7 km elevational gradient on Mt. Kilimanjaro, we quantify cross-taxon consensus in diversity gradients and evaluate predictors of diversity from single taxa to a multi-taxa community level. While single taxa show complex distribution patterns and respond to different environmental factors, scaling up diversity to the community level leads to an unambiguous support for temperature as the main predictor of species richness in both plants and animals. Our findings illuminate the influence of taxonomic coverage for models of diversity gradients and point to the importance of temperature for diversification and species coexistence in plant and animal communities.},
  language  = {en}
}
@article{DePalmaAbrahamczykAizenetal.2016,
  author    = {De Palma, Adriana and Abrahamczyk, Stefan and Aizen, Marcelo A. and Albrecht, Matthias and Basset, Yves and Bates, Adam and Blake, Robin J. and Boutin, C{\´e}line and Bugter, Rob and Connop, Stuart and Cruz-L{\´o}pez, Leopoldo and Cunningham, Saul A. and Darvill, Ben and Diek{\"o}tter, Tim and Dorn, Silvia and Downing, Nicola and Entling, Martin H. and Farwig, Nina and Felicioli, Antonio and Fonte, Steven J. and Fowler, Robert and Franzen, Markus Franz{\´e}n and Goulson, Dave and Grass, Ingo and Hanley, Mick E. and Hendrix, Stephen D. and Herrmann, Farina and Herzog, Felix and Holzschuh, Andrea and Jauker, Birgit and Kessler, Michael and Knight, M. E. and Kruess, Andreas and Lavelle, Patrick and Le F{\´e}on, Violette and Lentini, Pia and Malone, Louise A. and Marshall, Jon and Mart{\´i}nez Pach{\´o}n, Eliana and McFrederick, Quinn S. and Morales, Carolina L. and Mudri-Stojnic, Sonja and Nates-Parra, Guiomar and Nilsson, Sven G. and {\"O}ckinger, Erik and Osgathorpe, Lynne and Parra-H, Alejandro and Peres, Carlos A. and Persson, Anna S. and Petanidou, Theodora and Poveda, Katja and Power, Eileen F. and Quaranta, Marino and Quintero, Carolina and Rader, Romina and Richards, Miriam H. and Roulston, T'ai and Rousseau, Laurent and Sadler, Jonathan P. and Samneg{\aa}rd, Ulrika and Schellhorn, Nancy A. and Sch{\"u}epp, Christof and Schweiger, Oliver and Smith-Pardo, Allan H. and Steffan-Dewenter, Ingolf and Stout, Jane C. and Tonietto, Rebecca K. and Tscharntke, Teja and Tylianakis, Jason M. and Verboven, Hans A. F. and Vergara, Carlos H. and Verhulst, Jort and Westphal, Catrin and Yoon, Hyung Joo and Purvis, Andy},
  title     = {Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases},
  series = {Scientific Reports},
  volume    = {6},
  journal   = {Scientific Reports},
  doi       = {10.1038/srep31153},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167642},
  pages     = {31153},
  year      = {2016},
  abstract  = {Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises.},
  language  = {en}
}
@article{DrakulićFeldhaarLisičićetal.2016,
  author    = {Drakulić, Sanja and Feldhaar, Heike and Lisičić, Duje and Mioč, Mia and Cizelj, Ivan and Seiler, Michael and Spatz, Theresa and R{\"o}del, Mark-Oliver},
  title     = {Population-specific effects of developmental temperature on body condition and jumping performance of a widespread European frog},
  series = {Ecology and Evolution},
  volume    = {6},
  journal   = {Ecology and Evolution},
  number    = {10},
  doi       = {10.1002/ece3.2113},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-164960},
  pages     = {3115-3128},
  year      = {2016},
  abstract  = {All physiological processes of ectotherms depend on environmental temperature. Thus, adaptation of physiological mechanisms to the thermal environments is important for achieving optimal performance and fitness. The European Common Frog, Rana temporaria, is widely distributed across different thermal habitats. This makes it an exceptional model for studying the adaptations to different thermal conditions. We raised tadpoles from Germany and Croatia at two constant temperature treatments (15°C, 20°C), and under natural temperature fluctuations (in outdoor treatments), and tested how different developmental temperatures affected developmental traits, that is, length of larval development, morphometrics, and body condition, as well as jumping performance of metamorphs. Our results revealed population-specific differences in developmental time, body condition, and jumping performance. Croatian frogs developed faster in all treatments, were heavier, in better body condition, and had longer hind limbs and better jumping abilities than German metamorphs. The populations further differed in thermal sensitivity of jumping performance. While metamorphs from Croatia increased their jumping performance with higher temperatures, German metamorphs reached their performance maximum at lower temperatures. These population-specific differences in common environments indicate local genetic adaptation, with southern populations being better adapted to higher temperatures than those from north of the Alps.},
  language  = {en}
}
@article{KramerPiperEstevezetal.2016,
  author    = {Kramer, Susanne and Piper, Sophie and Estevez, Antonio and Carrington, Mark},
  title     = {Polycistronic trypanosome mRNAs are a target for the exosome},
  series = {Molecular and Biochemical Parasitology},
  volume    = {205},
  journal   = {Molecular and Biochemical Parasitology},
  number    = {1-2},
  doi       = {10.1016/j.molbiopara.2016.02.009},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-191350},
  pages     = {1-5},
  year      = {2016},
  abstract  = {Eukaryotic cells have several mRNA quality control checkpoints to avoid the production of aberrant proteins. Intron-containing mRNAs are actively degraded by the nuclear exosome, prevented from nuclear exit and, if these systems fail, degraded by the cytoplasmic NMD machinery. Trypanosomes have only two introns. However, they process mRNA5 from long polycistronic precursors by trans-splicing and polycistronic mRNA molecules frequently arise from any missed splice site. Here, we show that RNAi depletion of the trypanosome exosome, but not of the cytoplasmic 5'-3' exoribonuclease XRNA or the NMD helicase UPF1, causes accumulation of oligocistronic mRNA5. We have also revisited the localization of the trypanosome exosome by expressing eYFP-fusion proteins of the exosome subunits RRP44 and RRP6. Both proteins are significantly enriched in the nucleus. Together with published data, our data suggest a major nuclear function of the trypanosome exosome in rRNA, snoRNA and mRNA quality control.},
  language  = {en}
}
@article{MildnerRoces2016,
  author    = {Mildner, Stephanie and Roces, Flavio},
  title     = {Plasticity of Daily Behavioral Rhythms in Foragers and Nurses of the Ant Camponotus rufipes: Influence of Social Context and Feeding Times},
  series = {PLoS One},
  volume    = {12},
  journal   = {PLoS One},
  number    = {1},
  doi       = {10.1371/journal.pone.0169244},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-148010},
  pages     = {e0169244},
  year      = {2016},
  abstract  = {Daily activities within an ant colony need precise temporal organization, and an endogenous clock appears to be essential for such timing processes. A clock drives locomotor rhythms in isolated workers in a number of ant species, but its involvement in activities displayed in the social context is unknown. We compared locomotor rhythms in isolated individuals and behavioral rhythms in the social context of workers of the ant Camponotus rufipes. Both forager and nurse workers exhibited circadian rhythms in locomotor activity under constant conditions, indicating the involvement of an endogenous clock. Activity was mostly nocturnal and synchronized with the 12:12h light-dark-cycle. To evaluate whether rhythmicity was maintained in the social context and could be synchronized with non-photic zeitgebers such as feeding times, daily behavioral activities of single workers inside and outside the nest were quantified continuously over 24 hours in 1656 hours of video recordings. Food availability was limited to a short time window either at day or at night, thus mimicking natural conditions of temporally restricted food access. Most foragers showed circadian foraging behavior synchronized with food availability, either at day or nighttime. When isolated thereafter in single locomotor activity monitors, foragers mainly displayed arrhythmicity. Here, high mortality suggested potential stressful effects of the former restriction of food availability. In contrast, nurse workers showed high overall activity levels in the social context and performed their tasks all around the clock with no circadian pattern, likely to meet the needs of the brood. In isolation, the same individuals exhibited in turn strong rhythmic activity and nocturnality. Thus, endogenous activity rhythms were inhibited in the social context, and timing of daily behaviors was flexibly adapted to cope with task demands. As a similar socially-mediated plasticity in circadian rhythms was already shown in honey bees, the temporal organization in C. rufipes and honey bees appear to share similar basic features.},
  language  = {en}
}
@article{VieraElMerahbiNieswandtetal.2016,
  author    = {Viera, Jonathan Trujillo and El-Merahbi, Rabih and Nieswandt, Bernhard and Stegner, David and Sumara, Grzegorz},
  title     = {Phospholipases D1 and D2 Suppress Appetite and Protect against Overweight},
  series = {PLoS ONE},
  volume    = {11},
  journal   = {PLoS ONE},
  number    = {6},
  doi       = {10.1371/journal.pone.0157607},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-179729},
  year      = {2016},
  abstract  = {Obesity is a major risk factor predisposing to the development of peripheral insulin resistance and type 2 diabetes (T2D). Elevated food intake and/or decreased energy expenditure promotes body weight gain and acquisition of adipose tissue. Number of studies implicated phospholipase D (PLD) enzymes and their product, phosphatidic acid (PA), in regulation of signaling cascades controlling energy intake, energy dissipation and metabolic homeostasis. However, the impact of PLD enzymes on regulation of metabolism has not been directly determined so far. In this study we utilized mice deficient for two major PLD isoforms, PLD1 and PLD2, to assess the impact of these enzymes on regulation of metabolic homeostasis. We showed that mice lacking PLD1 or PLD2 consume more food than corresponding control animals. Moreover, mice deficient for PLD2, but not PLD1, present reduced energy expenditure. In addition, deletion of either of the PLD enzymes resulted in development of elevated body weight and increased adipose tissue content in aged animals. Consistent with the fact that elevated content of adipose tissue predisposes to the development of hyperlipidemia and insulin resistance, characteristic for the pre-diabetic state, we observed that Pld1\(^{-/-}\) and Pld2\(^{-/-}\) mice present elevated free fatty acids (FFA) levels and are insulin as well as glucose intolerant. In conclusion, our data suggest that deficiency of PLD1 or PLD2 activity promotes development of overweight and diabetes.},
  language  = {en}
}
@article{JoschinskiBeerHelfrichFoersteretal.2016,
  author    = {Joschinski, Jens and Beer, Katharina and Helfrich-F{\"o}rster, Charlotte and Krauss, Jochen},
  title     = {Pea Aphids (Hemiptera: Aphididae) Have Diurnal Rhythms When Raised Independently of a Host Plant},
  series = {Journal of Insect Science},
  volume    = {16},
  journal   = {Journal of Insect Science},
  number    = {1},
  doi       = {10.1093/jisesa/iew013},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-168783},
  pages     = {31},
  year      = {2016},
  abstract  = {Seasonal timing is assumed to involve the circadian clock, an endogenous mechanism to track time and measure day length. Some debate persists, however, and aphids were among the first organisms for which circadian clock involvement was questioned. Inferences about links to phenology are problematic, as the clock itself is little investigated in aphids. For instance, it is unknown whether aphids possess diurnal rhythms at all. Possibly, the close interaction with host plants prevents independent measurements of rhythmicity. We reared the pea aphid Acyrthosiphon pisum (Harris) on an artificial diet, and recorded survival, moulting, and honeydew excretion. Despite their plant-dependent life style, aphids were independently rhythmic under light-dark conditions. This first demonstration of diurnal aphid rhythms shows that aphids do not simply track the host plant's rhythmicity.},
  language  = {en}
}
@article{LichthardtKerscherDietzetal.2016,
  author    = {Lichthardt, Sven and Kerscher, Alexander and Dietz, Ulrich A. and Jurowich, Christian and Kunzmann, Volker and von Rahden, Burkhard H. A. and Germer, Christoph-Thomas and Wiegering, Armin},
  title     = {Original article: role of adjuvant chemotherapy in a perioperative chemotherapy regimen for gastric cancer},
  series = {BMC Cancer},
  volume    = {16},
  journal   = {BMC Cancer},
  number    = {650},
  doi       = {10.1186/s12885-016-2708-0},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147743},
  year      = {2016},
  abstract  = {Background Multimodal treatment strategies - perioperative chemotherapy (CTx) and radical surgery - are currently accepted as treatment standard for locally advanced gastric cancer. However, the role of adjuvant postoperative CTx (postCTx) in addition to neoadjuvant preoperative CTx (preCTx) in this setting remains controversial. Methods Between 4/2006 and 12/2013, 116 patients with locally advanced gastric cancer were treated with preCTx. 72 patients (62 \%), in whom complete tumor resection (R0, subtotal/total gastrectomy with D2-lymphadenectomy) was achieved, were divided into two groups, one of which receiving adjuvant therapy (n = 52) and one without (n = 20). These groups were analyzed with regard to survival and exclusion criteria for adjuvant therapy. Results Postoperative complications, as well as their severity grade, did not correlate with fewer postCTx cycles administered (p = n.s.). Long-term survival was shorter in patients receiving postCTx in comparison to patients without postCTx, but did not show statistical significance. In per protocol analysis by excluding two patients with perioperative death, a shorter 3-year survival rate was observed in patients receiving postCTx compared to patients without postCTx (3-year survival: 71.2 \% postCTx group vs. 90.0 \% non-postCTx group; p = 0.038). Conclusion These results appear contradicting to the anticipated outcome. While speculative, they question the value of post-CTx. Prospectively randomized studies are needed to elucidate the role of postCTx.},
  language  = {en}
}
@article{FeldbauerSchlegelWeissbeckeretal.2016,
  author    = {Feldbauer, Katrin and Schlegel, Jan and Weissbecker, Juliane and Sauer, Frank and Wood, Phillip G. and Bamberg, Ernst and Terpitz, Ulrich},
  title     = {Optochemokine Tandem for Light-Control of Intracellular Ca\(^{2+}\)},
  series = {PLoS ONE},
  volume    = {11},
  journal   = {PLoS ONE},
  number    = {10},
  doi       = {10.1371/journal.pone.0165344},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-178921},
  year      = {2016},
  abstract  = {An optochemokine tandem was developed to control the release of calcium from endosomes into the cytosol by light and to analyze the internalization kinetics of G-protein coupled receptors (GPCRs) by electrophysiology. A previously constructed rhodopsin tandem was re-engineered to combine the light-gated Ca\(^{2+}\)-permeable cation channel Channelrhodopsin-2(L132C), CatCh, with the chemokine receptor CXCR4 in a functional tandem protein tCXCR4/CatCh. The GPCR was used as a shuttle protein to displace CatCh from the plasma membrane into intracellular areas. As shown by patch-clamp measurements and confocal laser scanning microscopy, heterologously expressed tCXCR4/CatCh was internalized via the endocytic SDF1/CXCR4 signaling pathway. The kinetics of internalization could be followed electrophysiologically via the amplitude of the CatCh signal. The light-induced release of Ca\(^{2+}\) by tandem endosomes into the cytosol via CatCh was visualized using the Ca\(^{2+}\)-sensitive dyes rhod2 and rhod2-AM showing an increase of intracellular Ca\(^{2+}\) in response to light.},
  language  = {en}
}
@article{MederKoenigOzretićetal.2016,
  author    = {Meder, Lydia and K{\"o}nig, Katharina and Ozretić, Luka and Schultheis, Anne M. and Ueckeroth, Frank and Ade, Carsten P. and Albus, Kerstin and Boehm, Diana and Rommerscheidt-Fuss, Ursula and Florin, Alexandra and Buhl, Theresa and Hartmann, Wolfgang and Wolf, J{\"u}rgen and Merkelbach-Bruse, Sabine and Eilers, Martin and Perner, Sven and Heukamp, Lukas C. and Buettner, Reinhard},
  title     = {NOTCH, ASCL1, p53 and RB alterations define an alternative pathway driving neuroendocrine and small cell lung carcinomas},
  series = {International Journal of Cancer},
  volume    = {138},
  journal   = {International Journal of Cancer},
  number    = {4},
  doi       = {10.1002/ijc.29835},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-190853},
  pages     = {927-938},
  year      = {2016},
  abstract  = {Small cell lung cancers (SCLCs) and extrapulmonary small cell cancers (SCCs) are very aggressive tumors arising de novo as primary small cell cancer with characteristic genetic lesions in RB1 and TP53. Based on murine models, neuroendocrine stem cells of the terminal bronchioli have been postulated as the cellular origin of primary SCLC. However, both in lung and many other organs, combined small cell/non-small cell tumors and secondary transitions from non-small cell carcinomas upon cancer therapy to neuroendocrine and small cell tumors occur. We define features of "small cell-ness" based on neuroendocrine markers, characteristic RB1 and TP53 mutations and small cell morphology. Furthermore, here we identify a pathway driving the pathogenesis of secondary SCLC involving inactivating NOTCH mutations, activation of the NOTCH target ASCL1 and canonical WNT-signaling in the context of mutual bi-allelic RB1 and TP53 lesions. Additionaly, we explored ASCL1 dependent RB inactivation by phosphorylation, which is reversible by CDK5 inhibition. We experimentally verify the NOTCH-ASCL1-RB-p53 signaling axis in vitro and validate its activation by genetic alterations in vivo. We analyzed clinical tumor samples including SCLC, SCC and pulmonary large cell neuroendocrine carcinomas and adenocarcinomas using amplicon-based Next Generation Sequencing, immunohistochemistry and fluorescence in situ hybridization. In conclusion, we identified a novel pathway underlying rare secondary SCLC which may drive small cell carcinomas in organs other than lung, as well.},
  language  = {en}
}
@article{KunzWolfSchulzeetal.2016,
  author    = {Kunz, Meik and Wolf, Beat and Schulze, Harald and Atlan, David and Walles, Thorsten and Walles, Heike and Dandekar, Thomas},
  title     = {Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools},
  series = {Genes},
  volume    = {8},
  journal   = {Genes},
  number    = {1},
  doi       = {10.3390/genes8010008},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147990},
  pages     = {8},
  year      = {2016},
  abstract  = {Lung cancer is currently the leading cause of cancer related mortality due to late diagnosis and limited treatment intervention. Non-coding RNAs are not translated into proteins and have emerged as fundamental regulators of gene expression. Recent studies reported that microRNAs and long non-coding RNAs are involved in lung cancer development and progression. Moreover, they appear as new promising non-invasive biomarkers for early lung cancer diagnosis. Here, we highlight their potential as biomarker in lung cancer and present how bioinformatics can contribute to the development of non-invasive diagnostic tools. For this, we discuss several bioinformatics algorithms and software tools for a comprehensive understanding and functional characterization of microRNAs and long non-coding RNAs.},
  language  = {en}
}
@article{YadavSelvarajBenderetal.2016,
  author    = {Yadav, Preeti and Selvaraj, Bhuvaneish T. and Bender, Florian L. P. and Behringer, Marcus and Moradi, Mehri and Sivadasan, Rajeeve and Dombert, Benjamin and Blum, Robert and Asan, Esther and Sauer, Markus and Julien, Jean-Pierre and Sendtner, Michael},
  title     = {Neurofilament depletion improves microtubule dynamics via modulation of Stat3/stathmin signaling},
  series = {Acta Neuropathologica},
  volume    = {132},
  journal   = {Acta Neuropathologica},
  number    = {1},
  doi       = {10.1007/s00401-016-1564-y},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-188234},
  pages     = {93-110},
  year      = {2016},
  abstract  = {In neurons, microtubules form a dense array within axons, and the stability and function of this microtubule network is modulated by neurofilaments. Accumulation of neurofilaments has been observed in several forms of neurodegenerative diseases, but the mechanisms how elevated neurofilament levels destabilize axons are unknown so far. Here, we show that increased neurofilament expression in motor nerves of pmn mutant mice, a model of motoneuron disease, causes disturbed microtubule dynamics. The disease is caused by a point mutation in the tubulin-specific chaperone E (Tbce) gene, leading to an exchange of the most C-terminal amino acid tryptophan to glycine. As a consequence, the TBCE protein becomes instable which then results in destabilization of axonal microtubules and defects in axonal transport, in particular in motoneurons. Depletion of neurofilament increases the number and regrowth of microtubules in pmn mutant motoneurons and restores axon elongation. This effect is mediated by interaction of neurofilament with the stathmin complex. Accumulating neurofilaments associate with stathmin in axons of pmn mutant motoneurons. Depletion of neurofilament by Nefl knockout increases Stat3-stathmin interaction and stabilizes the microtubules in pmn mutant motoneurons. Consequently, counteracting enhanced neurofilament expression improves axonal maintenance and prolongs survival of pmn mutant mice. We propose that this mechanism could also be relevant for other neurodegenerative diseases in which neurofilament accumulation and loss of microtubules are prominent features.},
  language  = {en}
}
@article{ZhuShabalaCuinetal.2016,
  author    = {Zhu, Min and Shabala, Lana and Cuin, Tracey A and Huang, Xin and Zhou, Meixue and Munns, Rana and Shabala, Sergey},
  title     = {Nax loci affect SOS1-like Na\(^{+}\)/H\(^{+}\) exchanger expression and activity in wheat},
  series = {Journal of Experimental Botany},
  volume    = {67},
  journal   = {Journal of Experimental Botany},
  number    = {3},
  doi       = {10.1093/jxb/erv493},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-150236},
  pages     = {835-844},
  year      = {2016},
  abstract  = {Salinity stress tolerance in durum wheat is strongly associated with a plant's ability to control Na\(^{+}\) delivery to the shoot. Two loci, termed Nax1 and Nax2, were recently identified as being critical for this process and the sodium transporters HKT1;4 and HKT1;5 were identified as the respective candidate genes. These transporters retrieve Na\(^{+}\) from the xylem, thus limiting the rates of Na\(^{+}\) transport from the root to the shoot. In this work, we show that the Nax loci also affect activity and expression levels of the SOS1-like Na\(^{+}\)/H\(^{+}\) exchanger in both root cortical and stelar tissues. Net Na\(^{+}\) efflux measured in isolated steles from salt-treated plants, using the non-invasive ion flux measuring MIFE technique, decreased in the sequence: Tamaroi (parental line)>Nax1=Nax2>Nax1:Nax2 lines. This efflux was sensitive to amiloride (a known inhibitor of the Na\(^{+}\)/H\(^{+}\) exchanger) and was mirrored by net H\(^{+}\) flux changes. TdSOS1 relative transcript levels were 6-10-fold lower in Nax lines compared with Tamaroi. Thus, it appears that Nax loci confer two highly complementary mechanisms, both of which contribute towards reducing the xylem Na\(^{+}\) content. One enhances the retrieval of Na\(^{+}\) back into the root stele via HKT1;4 or HKT1;5, whilst the other reduces the rate of Na\(^{+}\) loading into the xylem via SOS1. It is suggested that such duality plays an important adaptive role with greater versatility for responding to a changing environment and controlling Na\(^{+}\) delivery to the shoot.},
  language  = {en}
}
@article{HartelGloggerJonesetal.2016,
  author    = {Hartel, Andreas J.W. and Glogger, Marius and Jones, Nicola G. and Abuillan, Wasim and Batram, Christopher and Hermann, Anne and Fenz, Susanne F. and Tanaka, Motomu and Engstler, Markus},
  title     = {N-glycosylation enables high lateral mobility of GPI-anchored proteins at a molecular crowding threshold},
  series = {Nature Communications},
  volume    = {7},
  journal   = {Nature Communications},
  doi       = {10.1038/ncomms12870},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-171368},
  year      = {2016},
  abstract  = {The protein density in biological membranes can be extraordinarily high, but the impact of molecular crowding on the diffusion of membrane proteins has not been studied systematically in a natural system. The diversity of the membrane proteome of most cells may preclude systematic studies. African trypanosomes, however, feature a uniform surface coat that is dominated by a single type of variant surface glycoprotein (VSG). Here we study the density-dependence of the diffusion of different glycosylphosphatidylinositol-anchored VSG-types on living cells and in artificial membranes. Our results suggest that a specific molecular crowding threshold (MCT) limits diffusion and hence affects protein function. Obstacles in the form of heterologous proteins compromise the diffusion coefficient and the MCT. The trypanosome VSG-coat operates very close to its MCT. Importantly, our experiments show that N-linked glycans act as molecular insulators that reduce retarding intermolecular interactions allowing membrane proteins to function correctly even when densely packed.},
  language  = {en}
}
@article{WeisschuhMayerStrometal.2016,
  author    = {Weisschuh, Nicole and Mayer, Anja K. and Strom, Tim M. and Kohl, Susanne and Gl{\"o}ckle, Nicola and Schubach, Max and Andreasson, Sten and Bernd, Antje and Birch, David G. and Hamel, Christian P. and Heckenlively, John R. and Jacobson, Samuel G. and Kamme, Christina and Kellner, Ulrich and Kunstmann, Erdmute and Maffei, Pietro and Reiff, Charlotte M. and Rohrschneider, Klaus and Rosenberg, Thomas and Rudolph, G{\"u}nther and V{\´a}mos, Rita and Vars{\´a}nyi, Bal{\´a}zs and Weleber, Richard G. and Wissinger, Bernd},
  title     = {Mutation Detection in Patients with Retinal Dystrophies Using Targeted Next Generation Sequencing},
  series = {PLoS ONE},
  volume    = {11},
  journal   = {PLoS ONE},
  number    = {1},
  doi       = {10.1371/journal.pone.0145951},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167398},
  pages     = {e0145951},
  year      = {2016},
  abstract  = {Retinal dystrophies (RD) constitute a group of blinding diseases that are characterized by clinical variability and pronounced genetic heterogeneity. The different nonsyndromic and syndromic forms of RD can be attributed to mutations in more than 200 genes. Consequently, next generation sequencing (NGS) technologies are among the most promising approaches to identify mutations in RD. We screened a large cohort of patients comprising 89 independent cases and families with various subforms of RD applying different NGS platforms. While mutation screening in 50 cases was performed using a RD gene capture panel, 47 cases were analyzed using whole exome sequencing. One family was analyzed using whole genome sequencing. A detection rate of 61\% was achieved including mutations in 34 known and two novel RD genes. A total of 69 distinct mutations were identified, including 39 novel mutations. Notably, genetic findings in several families were not consistent with the initial clinical diagnosis. Clinical reassessment resulted in refinement of the clinical diagnosis in some of these families and confirmed the broad clinical spectrum associated with mutations in RD genes.},
  language  = {en}
}
@article{AhmedZeeshanDandekar2016,
  author    = {Ahmed, Zeeshan and Zeeshan, Saman and Dandekar, Thomas},
  title     = {Mining biomedical images towards valuable information retrieval in biomedical and life sciences},
  series = {Database - The Journal of Biological Databases and Curation},
  volume    = {2016},
  journal   = {Database - The Journal of Biological Databases and Curation},
  doi       = {10.1093/database/baw118},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-162697},
  pages     = {baw118},
  year      = {2016},
  abstract  = {Biomedical images are helpful sources for the scientists and practitioners in drawing significant hypotheses, exemplifying approaches and describing experimental results in published biomedical literature. In last decades, there has been an enormous increase in the amount of heterogeneous biomedical image production and publication, which results in a need for bioimaging platforms for feature extraction and analysis of text and content in biomedical images to take advantage in implementing effective information retrieval systems. In this review, we summarize technologies related to data mining of figures. We describe and compare the potential of different approaches in terms of their developmental aspects, used methodologies, produced results, achieved accuracies and limitations. Our comparative conclusions include current challenges for bioimaging software with selective image mining, embedded text extraction and processing of complex natural language queries.},
  language  = {en}
}
@article{HeldBerzHensgenetal.2016,
  author    = {Held, Martina and Berz, Annuska and Hensgen, Ronja and Muenz, Thomas S. and Scholl, Christina and R{\"o}ssler, Wolfgang and Homberg, Uwe and Pfeiffer, Keram},
  title     = {Microglomerular Synaptic Complexes in the Sky-Compass Network of the Honeybee Connect Parallel Pathways from the Anterior Optic Tubercle to the Central Complex},
  series = {Frontiers in Behavioral Neuroscience},
  volume    = {10},
  journal   = {Frontiers in Behavioral Neuroscience},
  number    = {186},
  doi       = {10.3389/fnbeh.2016.00186},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-165080},
  year      = {2016},
  abstract  = {While the ability of honeybees to navigate relying on sky-compass information has been investigated in a large number of behavioral studies, the underlying neuronal system has so far received less attention. The sky-compass pathway has recently been described from its input region, the dorsal rim area (DRA) of the compound eye, to the anterior optic tubercle (AOTU). The aim of this study is to reveal the connection from the AOTU to the central complex (CX). For this purpose, we investigated the anatomy of large microglomerular synaptic complexes in the medial and lateral bulbs (MBUs/LBUs) of the lateral complex (LX). The synaptic complexes are formed by tubercle-lateral accessory lobe neuron 1 (TuLAL1) neurons of the AOTU and GABAergic tangential neurons of the central body's (CB) lower division (TL neurons). Both TuLAL1 and TL neurons strongly resemble neurons forming these complexes in other insect species. We further investigated the ultrastructure of these synaptic complexes using transmission electron microscopy. We found that single large presynaptic terminals of TuLAL1 neurons enclose many small profiles (SPs) of TL neurons. The synaptic connections between these neurons are established by two types of synapses: divergent dyads and divergent tetrads. Our data support the assumption that these complexes are a highly conserved feature in the insect brain and play an important role in reliable signal transmission within the sky-compass pathway.},
  language  = {en}
}