TY  - JOUR
A1  - Lamatsch, Dunja K.
A1  - Adolfsson, Sofia
A1  - Senior, Alistair M.
A1  - Christiansen, Guntram
A1  - Pichler, Maria
A1  - Ozaki, Yuichi
A1  - Smeds, Linnea
A1  - Schartl, Manfred
A1  - Nakagawa, Shinichi
T1  - A transcriptome derived female-specific marker from the invasive Western mosquitofish (Gambusia affinis)
JF  - PLoS ONE
N2  - Sex-specific markers are a prerequisite for understanding reproductive biology, genetic factors involved in sex differences, mechanisms of sex determination, and ultimately the evolution of sex chromosomes. The Western mosquitofish, Gambusia affinis, may be considered a model species for sex-chromosome evolution, as it displays female heterogamety (ZW/ZZ), and is also ecologically interesting as a worldwide invasive species. Here, de novo RNA-sequencing on the gonads of sexually mature G. affinis was used to identify contigs that were highly transcribed in females but not in males (i.e., transcripts with ovary-specific expression). Subsequently, 129 primer pairs spanning 79 contigs were tested by PCR to identify sex-specific transcripts. Of those primer pairs, one female-specific DNA marker was identified, Sanger sequenced and subsequently validated in 115 fish. Sequence analyses revealed a high similarity between the identified sex-specific marker and the 3' UTR of the aminomethyl transferase (amt) gene of the closely related platyfish (Xiphophorus maculatus). This is the first time that RNA-seq has been used to successfully characterize a sex-specific marker in a fish species in the absence of a genome map. Additionally, the identified sex-specific marker represents one of only a handful of such markers in fishes.
KW  - sex chromosome evolution
KW  - linkage map
KW  - determination locus
KW  - poeciliid fishes
KW  - heterogamety
KW  - Cynoglossus semilaevis
KW  - determining genes
KW  - Y chromosome
KW  - sequence alignment
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-144004
VL  - 10
IS  - 2
ER  - 
TY  - JOUR
A1  - Basset, Yves
A1  - Cizek, Lukas
A1  - Cuénoud, Philippe
A1  - Didham, Raphael K.
A1  - Novotny, Vojtech
A1  - Ødegaard, Frode
A1  - Roslin, Tomas
A1  - Tishechkin, Alexey K.
A1  - Schmidl, Jürgen
A1  - Winchester, Neville N.
A1  - Roubik, David W.
A1  - Aberlenc, Henri-Pierre
A1  - Bail, Johannes
A1  - Barrios, Hector
A1  - Bridle, Jonathan R.
A1  - Castaño-Meneses, Gabriela
A1  - Corbara, Bruno
A1  - Curletti, Gianfranco
A1  - da Rocha, Wesley Duarte
A1  - De Bakker, Domir
A1  - Delabie, Jacques H. C.
A1  - Dejean, Alain
A1  - Fagan, Laura L.
A1  - Floren, Andreas
A1  - Kitching, Roger L.
A1  - Medianero, Enrique
A1  - de Oliveira, Evandro Gama
A1  - Orivel, Jerome
A1  - Pollet, Marc
A1  - Rapp, Mathieu
A1  - Ribeiro, Servio P.
A1  - Roisin, Yves
A1  - Schmidt, Jesper B.
A1  - Sørensen, Line
A1  - Lewinsohn, Thomas M.
A1  - Leponce, Maurice
T1  - Arthropod Distribution in a Tropical Rainforest: Tackling a Four Dimensional Puzzle
JF  - PLoS ONE
N2  - Quantifying the spatio-temporal distribution of arthropods in tropical rainforests represents a first step towards scrutinizing the global distribution of biodiversity on Earth. To date most studies have focused on narrow taxonomic groups or lack a design that allows partitioning of the components of diversity. Here, we consider an exceptionally large dataset (113,952 individuals representing 5,858 species), obtained from the San Lorenzo forest in Panama, where the phylogenetic breadth of arthropod taxa was surveyed using 14 protocols targeting the soil, litter, understory, lower and upper canopy habitats, replicated across seasons in 2003 and 2004. This dataset is used to explore the relative influence of horizontal, vertical and seasonal drivers of arthropod distribution in this forest. We considered arthropod abundance, observed and estimated species richness, additive decomposition of species richness, multiplicative partitioning of species diversity, variation in species composition, species turnover and guild structure as components of diversity. At the scale of our study (2km of distance, 40m in height and 400 days), the effects related to the vertical and seasonal dimensions were most important. Most adult arthropods were collected from the soil/litter or the upper canopy and species richness was highest in the canopy. We compared the distribution of arthropods and trees within our study system. Effects related to the seasonal dimension were stronger for arthropods than for trees. We conclude that: (1) models of beta diversity developed for tropical trees are unlikely to be applicable to tropical arthropods; (2) it is imperative that estimates of global biodiversity derived from mass collecting of arthropods in tropical rainforests embrace the strong vertical and seasonal partitioning observed here; and (3) given the high species turnover observed between seasons, global climate change may have severe consequences for rainforest arthropods.
KW  - trees
KW  - species richness
KW  - beta-diveristy
KW  - strategy
KW  - turnover
KW  - similarity
KW  - biodiversity
KW  - specialization
KW  - herbivorous insects
KW  - assemblages
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-136393
VL  - 10
IS  - 12
ER  - 
TY  - JOUR
A1  - Paul, Mila M.
A1  - Pauli, Martin
A1  - Ehmann, Nadine
A1  - Hallermann, Stefan
A1  - Sauer, Markus
A1  - Kittel, Robert J.
A1  - Heckmann, Manfred
T1  - Bruchpilot and Synaptotagmin collaborate to drive rapid glutamate release and active zone differentiation
JF  - Frontiers in Cellular Neuroscience
N2  - The active zone (AZ) protein Bruchpilot (Brp) is essential for rapid glutamate release at Drosophila melanogaster neuromuscular junctions (NMJs). Quantal time course and measurements of action potential-waveform suggest that presynaptic fusion mechanisms are altered in brp null mutants (brp\(^{69}\)). This could account for their increased evoked excitatory postsynaptic current (EPSC) delay and rise time (by about 1 ms). To test the mechanism of release protraction at brp\(^{69}\) AZs, we performed knock-down of Synaptotagmin-1 (Syt) via RNAi (syt\(^{KD}\)) in wildtype (wt), brp\(^{69}\) and rab3 null mutants (rab3\(^{rup}\)), where Brp is concentrated at a small number of AZs. At wt and rab3\(^{rup}\) synapses, syt\(^{KD}\) lowered EPSC amplitude while increasing rise time and delay, consistent with the role of Syt as a release sensor. In contrast, syt\(^{KD}\) did not alter EPSC amplitude at brp\(^{69}\) synapses, but shortened delay and rise time. In fact, following syt\(^{KD}\), these kinetic properties were strikingly similar in wt and brp\(^{69}\), which supports the notion that Syt protracts release at brp\(^{69}\) synapses. To gain insight into this surprising role of Syt at brp\(^{69}\) AZs, we analyzed the structural and functional differentiation of synaptic boutons at the NMJ. At tonic type Ib motor neurons, distal boutons contain more AZs, more Brp proteins per AZ and show elevated and accelerated glutamate release compared to proximal boutons. The functional differentiation between proximal and distal boutons is Brp-dependent and reduced after syt\(^{KD}\). Notably, syt\(^{KD}\) boutons are smaller, contain fewer Brp positive AZs and these are of similar number in proximal and distal boutons. In addition, super-resolution imaging via dSTORM revealed that syt\(^{KD}\) increases the number and alters the spatial distribution of Brp molecules at AZs, while the gradient of Brp proteins per AZ is diminished. In summary, these data demonstrate that normal structural and functional differentiation of Drosophila AZs requires concerted action of Brp and Syt.
KW  - neuromuscular junction
KW  - Bruchpilot
KW  - synaptic delay
KW  - dSTORM
KW  - synaptotagmin
KW  - presynaptic differentiation
KW  - neurotransmitter release
KW  - active zone
KW  - synaptic transmission
KW  - fluorescent probes
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-148988
VL  - 9
IS  - 29
ER  - 
TY  - JOUR
A1  - Karl, Stefan
A1  - Dandekar, Thomas
T1  - Convergence behaviour and control in non-linear biological networks
JF  - Scientific Reports
N2  - Control of genetic regulatory networks is challenging to define and quantify. Previous control centrality metrics, which aim to capture the ability of individual nodes to control the system, have been found to suffer from plausibility and applicability problems. Here we present a new approach to control centrality based on network convergence behaviour, implemented as an extension of our genetic regulatory network simulation framework Jimena (http://stefan-karl.de/jimena). We distinguish three types of network control, and show how these mathematical concepts correspond to experimentally verified node functions and signalling pathways in immunity and cell differentiation: Total control centrality quantifies the impact of node mutations and identifies potential pharmacological targets such as genes involved in oncogenesis (e.g. zinc finger protein GLI2 or bone morphogenetic proteins in chondrocytes). Dynamic control centrality describes relaying functions as observed in signalling cascades (e.g. src kinase or Jak/Stat pathways). Value control centrality measures the direct influence of the value of the node on the network (e.g. Indian hedgehog as an essential regulator of proliferation in chondrocytes). Surveying random scale-free networks and biological networks, we find that control of the network resides in few high degree driver nodes and networks can be controlled best if they are sparsely connected.
KW  - complex networks
KW  - control profiles
KW  - differentiation
KW  - pathways
KW  - tumors
KW  - models
KW  - centrality
KW  - chondrosarcoma
KW  - transcriptional regulation
KW  - regulatory networks
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-148510
VL  - 5
IS  - 09746
ER  - 
TY  - JOUR
A1  - Joschinski, Jens
A1  - Hovestadt, Thomas
A1  - Krauss, Jochen
T1  - Coping with shorter days: do phenology shifts constrain aphid fitness?
JF  - PeerJ
N2  - Climate change can alter the phenology of organisms. It may thus lead seasonal organisms to face different day lengths than in the past, and the fitness consequences of these changes are as yet unclear. To study such effects, we used the pea aphid Acyrthosiphon pisum as a model organism, as it has obligately asexual clones which can be used to study day length effects without eliciting a seasonal response. We recorded life-history traits under short and long days, both with two realistic temperature cycles with means differing by 2 °C. In addition, we measured the population growth of aphids on their host plant Pisum sativum. We show that short days reduce fecundity and the length of the reproductive period of aphids. Nevertheless, this does not translate into differences at the population level because the observed fitness costs only become apparent late in the individual's life. As expected, warm temperature shortens the development time by 0.7 days/°C, leading to faster generation times. We found no interaction of temperature and day length. We conclude that day length changes cause only relatively mild costs, which may not decelerate the increase in pest status due to climate change.
KW  - Homoptera aphididae
KW  - clock reproduction ecology
KW  - phenotypic plasticity
KW  - phenology shifts
KW  - insect timing
KW  - physiological constraints
KW  - day length
KW  - circadian rhythms
KW  - Acyrthosiphon pisum
KW  - climate change
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-148382
VL  - 3
IS  - e1103
ER  - 
TY  - JOUR
A1  - Kleijn, David
A1  - Winfree, Rachael
A1  - Bartomeus, Ignasi
A1  - Carvalheiro, Luísa G.
A1  - Henry, Mickael
A1  - Isaacs, Rufus
A1  - Klein, Alexandra-Maria
A1  - Kremen, Claire
A1  - M'Gonigle, Leithen K.
A1  - Rader, Romina
A1  - Ricketts, Taylor H.
A1  - Williams, Neal M.
A1  - Adamson, Nancy Lee
A1  - Ascher, John S.
A1  - Báldi, András
A1  - Batáry, Péter
A1  - Benjamin, Faye
A1  - Biesmeijer, Jacobus C.
A1  - Blitzer, Eleanor J.
A1  - Bommarco, Riccardo
A1  - Brand, Mariette R.
A1  - Bretagnolle, Vincent
A1  - Button, Lindsey
A1  - Cariveau, Daniel P.
A1  - Chifflet, Rémy
A1  - Colville, Jonathan F.
A1  - Danforth, Bryan N.
A1  - Elle, Elizabeth
A1  - Garratt, Michael P. D.
A1  - Herzog, Felix
A1  - Holzschuh, Andrea
A1  - Howlett, Brad G.
A1  - Jauker, Frank
A1  - Jha, Shalene
A1  - Knop, Eva
A1  - Krewenka, Kristin M.
A1  - Le Féon, Violette
A1  - Mandelik, Yael
A1  - May, Emily A.
A1  - Park, Mia G.
A1  - Pisanty, Gideon
A1  - Reemer, Menno
A1  - Riedinger, Verena
A1  - Rollin, Orianne
A1  - Rundlöf, Maj
A1  - Sardiñas, Hillary S.
A1  - Scheper, Jeroen
A1  - Sciligo, Amber R.
A1  - Smith, Henrik G.
A1  - Steffan-Dewenter, Ingolf
A1  - Thorp, Robbin
A1  - Tscharntke, Teja
A1  - Verhulst, Jort
A1  - Viana, Blandina F.
A1  - Vaissière, Bernard E.
A1  - Veldtman, Ruan
A1  - Ward, Kimiora L.
A1  - Westphal, Catrin
A1  - Potts, Simon G.
T1  - Delivery of crop pollination services is an insufficient argument for wild pollinator conservation
JF  - Nature Communications
N2  - There is compelling evidence that more diverse ecosystems deliver greater benefits to people, and these ecosystem services have become a key argument for biodiversity conservation. However, it is unclear how much biodiversity is needed to deliver ecosystem services in a cost- effective way. Here we show that, while the contribution of wild bees to crop production is significant, service delivery is restricted to a limited subset of all known bee species. Across crops, years and biogeographical regions, crop-visiting wild bee communities are dominated by a small number of common species, and threatened species are rarely observed on crops. Dominant crop pollinators persist under agricultural expansion and many are easily enhanced by simple conservation measures, suggesting that cost- effective management strategies to promote crop pollination should target a different set of species than management strategies to promote threatened bees. Conserving the biological diversity of bees therefore requires more than just ecosystem-service-based arguments.
KW  - ecosystem services
KW  - european countries
KW  - abundance
KW  - native bees
KW  - biodiversity conservation
KW  - plant diversity
KW  - fruit set
KW  - productivity
KW  - decline
KW  - pollen
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-151879
VL  - 6
IS  - 7414
ER  - 
TY  - JOUR
A1  - Ott, Christine
A1  - Dorsch, Eva
A1  - Fraunholz, Martin
A1  - Straub, Sebastian
A1  - Kozjak-Pavlovic, Vera
T1  - Detailed Analysis of the Human Mitochondrial Contact Site Complex Indicate a Hierarchy of Subunits
JF  - PLoS One
N2  - Mitochondrial inner membrane folds into cristae, which significantly increase its surface and are important for mitochondrial function. The stability of cristae depends on the mitochondrial contact site (MICOS) complex. In human mitochondria, the inner membrane MICOS complex interacts with the outer membrane sorting and assembly machinery (SAM) complex, to form the mitochondrial intermembrane space bridging complex (MIB). We have created knockdown cell lines of most of the MICOS and MIB components and have used them to study the importance of the individual subunits for the cristae formation and complex stability. We show that the most important subunits of the MIB complex in human mitochondria are Mic60/Mitofilin, Mic19/CHCHD3 and an outer membrane component Sam50. We provide additional proof that ApoO indeed is a subunit of the MICOS and MIB complexes and propose the name Mic23 for this protein. According to our results, Mic25/CHCHD6, Mic27/ApoOL and Mic23/ApoO appear to be periphery subunits of the MICOS complex, because their depletion does not affect cristae morphology or stability of other components.
KW  - co-immunoprecipitation
KW  - motor proteins
KW  - mitochondria
KW  - membrane potential
KW  - membrane proteins
KW  - protein complexes
KW  - mitochondrial membrane
KW  - outer membrane proteins
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-125347
VL  - 10
IS  - 3
ER  - 
TY  - JOUR
A1  - Lakovic, Milica
A1  - Poethke, Hans-Joachim
A1  - Hovestadt, Thomas
T1  - Dispersal timing: Emigration of insects living in patchy environments
JF  - PLoS One
N2  - Dispersal is a life-history trait affecting dynamics and persistence of populations; it evolves under various known selective pressures. Theoretical studies on dispersal typically assume 'natal dispersal', where individuals emigrate right after birth. But emigration may also occur during a later moment within a reproductive season ('breeding dispersal'). For example, some female butterflies first deposit eggs in their natal patch before migrating to other site(s) to continue egg-laying there. How breeding compared to natal dispersal influences the evolution of dispersal has not been explored. To close this gap we used an individual-based simulation approach to analyze (i) the evolution of timing of breeding dispersal in annual organisms, (ii) its influence on dispersal (compared to natal dispersal). Furthermore, we tested (iii) its performance in direct evolutionary contest with individuals following a natal dispersal strategy. Our results show that evolution should typically result in lower dispersal under breeding dispersal, especially when costs of dispersal are low and population size is small. By distributing offspring evenly across two patches, breeding dispersal allows reducing direct sibling competition in the next generation whereas natal dispersal can only reduce trans-generational kin competition by producing highly dispersive offspring in each generation. The added benefit of breeding dispersal is most prominent in patches with small population sizes. Finally, the evolutionary contests show that a breeding dispersal strategy would universally out-compete natal dispersal.
KW  - animal migration
KW  - statistical disperison
KW  - organismal evolution
KW  - animal sexual behavior
KW  - habitats
KW  - insects
KW  - carrying capacity
KW  - moths and butterflies
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-126466
VL  - 10
IS  - 7
ER  - 
TY  - JOUR
A1  - Floren, Andreas
A1  - Krüger, Dirk
A1  - Müller, Tobias
A1  - Dittrich, Marcus
A1  - Rudloff, Renate
A1  - Hoppe, Björn
A1  - Linsenmair, Karl Eduard
T1  - Diversity and interactions of wood-inhabiting fungi and beetles after deadwood enrichment
JF  - PLoS ONE
N2  - Freshly cut beech deadwood was enriched in the canopy and on the ground in three cultural landscapes in Germany (Swabian Alb, Hainich-Dun, Schorfheide-Chorin) in order to analyse the diversity, distribution and interaction of wood-inhabiting fungi and beetles. After two years of wood decay 83 MOTUs (Molecular Operational Taxonomic Units) from 28 wood samples were identified. Flight Interception Traps (FITs) installed adjacent to the deadwood enrichments captured 29.465 beetles which were sorted to 566 species. Geographical 'region' was the main factor determining both beetle and fungal assemblages. The proportions of species occurring in all regions were low. Statistic models suggest that assemblages of both taxa differed between stratum and management praxis but their strength varied among regions. Fungal assemblages in Hainich-Dun, for which the data was most comprehensive, discriminated unmanaged from extensively managed and age-class forests (even-aged timber management) while canopy communities differed not from those near the ground. In contrast, the beetle assemblages at the same sites showed the opposite pattern. We pursued an approach in the search for fungus-beetle associations by computing cross correlations and visualize significant links in a network graph. These correlations can be used to formulate hypotheses on mutualistic relationships for example in respect to beetles acting as vectors of fungal spores.
KW  - european beech forests
KW  - bark beetles
KW  - management
KW  - decay
KW  - ecology
KW  - norway spruce
KW  - substrate quality
KW  - communities
KW  - rare
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-145129
VL  - 10
IS  - 11
ER  - 
TY  - JOUR
A1  - Wolf, Beat
A1  - Kuonen, Pierre
A1  - Dandekar, Thomas
A1  - Atlan, David
T1  - DNAseq workflow in a diagnostic context and an example of a user friendly implementation
JF  - BioMed Research International
N2  - Over recent years next generation sequencing (NGS) technologies evolved from costly tools used by very few, to a much more accessible and economically viable technology. Through this recently gained popularity, its use-cases expanded from research environments into clinical settings. But the technical know-how and infrastructure required to analyze the data remain an obstacle for a wider adoption of this technology, especially in smaller laboratories. We present GensearchNGS, a commercial DNAseq software suite distributed by Phenosystems SA. The focus of GensearchNGS is the optimal usage of already existing infrastructure, while keeping its use simple. This is achieved through the integration of existing tools in a comprehensive software environment, as well as custom algorithms developed with the restrictions of limited infrastructures in mind. This includes the possibility to connect multiple computers to speed up computing intensive parts of the analysis such as sequence alignments. We present a typical DNAseq workflow for NGS data analysis and the approach GensearchNGS takes to implement it. The presented workflow goes from raw data quality control to the final variant report. This includes features such as gene panels and the integration of online databases, like Ensembl for annotations or Cafe Variome for variant sharing.
KW  - next generation sequencing
KW  - genome browser
KW  - mutation
KW  - algorithm
KW  - database
KW  - format
KW  - discovery
KW  - exome
KW  - variants
KW  - alignment
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-144527
IS  - 403497
ER  -