Succession, restoration, and management of dry grasslands - Special Feature with contributions from the 7th European Dry Grassland Meeting 2010 in Smolenice
- We first report from the 7th European Dry Grassland Meeting held 27 May to 1 June 2010 in Smolenice, Slovakia, devoted to the main topic “Succession, restoration and management of dry grasslands”. Apart from the scientific programme and the excursions, we also summarise the outcomes of the General Assembly of the EDGG and present the Smolenice Grassland Declaration. Then we take stock of the dynamic development of the European Dry Grassland Group (EDGG), report on its activities during the past year, and announce its future plans. Finally, we give a short introduction to the four articles of this Special Feature, which deal with biodiversity patterns, vegetation classification, and dynamics of dry grassland habitats. One presents a detailed phytosociological study of the xeric and mesic grasslands of the Slovak part of the Biele Karpaty Mts. The second provides a new numeric approach to the assignment of relevés to syntaxa and exemplifies this in a case study for the delimitation of the classes Festuco-Brometea against Trifolio-Geranietea sanguinei in Austria. The third article investigates the septennial impact of mouflon grazing and weather on dry grassland plant communities in dry grassland patches of the Czech Republic. The fourth article deals with long-term abandonment of grasslands in Central Slovakia and shows the importance of vegetation structure, ecological stability, and low-disturbance regime for specific ant assemblages.
FRET-Assisted Determination of CLN3 Membrane Topology
Mika O. Ruonala
- Juvenile neuronal ceroid lipofuscinosis (JNCL) is caused by mutations in the CLN3 gene, which encodes for a putative lysosomal transmembrane protein with thus far undescribed structure and function. Here we investigate the membrane topology of human CLN3 protein with a combination of advanced molecular cloning, spectroscopy, and in silico computation. Using the transposomics cloning method we first created a library of human CLN3 cDNA clones either with a randomly inserted eGFP, a myc-tag, or both. The functionality of the clones was evaluated by assessing their ability to revert a previously reported lysosomal phenotype in immortalized cerebellar granular cells derived from Cln3Δex7/8 mice (CbCln3Δex7/8). The double-tagged clones were expressed in HeLa cells, and FRET was measured between the donor eGFP and an acceptor DyLight547 coupled to a monoclonal α-myc antibody to assess their relative membrane orientation. The data were used together with previously reported experimental data to compile a constrained membrane topology model for hCLN3 using TOPCONS consensus membrane prediction algorithm. Our model with six transmembrane domains and cytosolic N- and C-termini largely agrees with those previously suggested but differs in terms of the transmembrane domain positions as well as in the size of the luminal loops. This finding improves understanding the function of the native hCLN3 protein.
An Illumina metabarcoding pipeline for fungi
- High-throughput metabarcoding studies on fungi and other eukaryotic microorganisms are rapidly becoming more frequent and more complex, requiring researchers to handle ever increasing amounts of raw sequence data. Here, we provide a flexible pipeline for pruning and analyzing fungal barcode (ITS rDNA) data generated as paired-end reads on Illumina MiSeq sequencers. The pipeline presented includes specific steps fine-tuned for ITS, that are mostly missing from pipelines developed for prokaryotes. It (1) employs state of the art programs and follows best practices in fungal high-throughput metabarcoding; (2) consists of modules and scripts easily modifiable by the user to ensure maximum flexibility with regard to specific needs of a project or future methodological developments; and (3) is straightforward to use, also in classroom settings. We provide detailed descriptions and revision techniques for each step, thus giving the user maximum control over data treatment and avoiding a black-box approach. Employing this pipeline will improve and speed up the tedious and error-prone process of cleaning fungal Illumina metabarcoding data.
Identification and characterization of RNA guanine-quadruplex binding proteins
Annekathrin von Hacht
- Guanine quadruplex (G-quadruplex) motifs in the 5′ untranslated region (5′-UTR) of mRNAs were recently shown to influence the efficiency of translation. In the present study, we investigate the interaction between cellular proteins and the G-quadruplexes located in two mRNAs (MMP16 and ARPC2). Formation of the G-quadruplexes was confirmed by biophysical characterization and the inhibitory activity on translation was shown by luciferase reporter assays. In experiments with whole cell extracts from different eukaryotic cell lines, G-quadruplex-binding proteins were isolated by pull-down assays and subsequently identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. The binding partners of the RNA G-quadruplexes we discovered included several heterogenous nuclear ribonucleoproteins, ribosomal proteins, and splicing factors, as well as other proteins that have previously not been described to interact with nucleic acids. While most of the proteins were specific for either of the investigated G-quadruplexes, some of them bound to both motifs. Selected candidate proteins were subsequently produced by recombinant expression and dissociation constants for the interaction between the proteins and RNA G-quadruplexes in the low nanomolar range were determined by surface plasmon resonance spectroscopy. The present study may thus help to increase our understanding of the mechanisms by which G-quadruplexes regulate translation.
Do listeners recover "deleted" final /t/ in German?
- Reduction and deletion processes occur regularly in conversational speech. A segment that is affected by such reduction and deletion processes in many Germanic languages (e.g., Dutch, English, German) is /t/. There are similarities concerning the factors that influence the likelihood of final /t/ to get deleted, such as segmental context. However, speakers of different languages differ with respect to the acoustic cues they leave in the speech signal when they delete final /t/. German speakers usually lengthen a preceding /s/ when they delete final /t/. This article investigates to what extent German listeners are able to reconstruct /t/ when they are presented with fragments of words where final /t/ has been deleted. It aims also at investigating whether the strategies that are used by German depend on the length of /s/, and therefore whether listeners are using language-specific cues. Results of a forced-choice segment detection task suggest that listeners are able to reconstruct deleted final /t/ in about 45% of the times. The length of /s/ plays some role in the reconstruction, however, it does not explain the behavior of German listeners completely.
Efficient Transfer Entropy Analysis of Non-Stationary Neural Time Series
Francisco J. Díaz-Pernas
- Information theory allows us to investigate information processing in neural systems in terms of information transfer, storage and modification. Especially the measure of information transfer, transfer entropy, has seen a dramatic surge of interest in neuroscience. Estimating transfer entropy from two processes requires the observation of multiple realizations of these processes to estimate associated probability density functions. To obtain these necessary observations, available estimators typically assume stationarity of processes to allow pooling of observations over time. This assumption however, is a major obstacle to the application of these estimators in neuroscience as observed processes are often non-stationary. As a solution, Gomez-Herrero and colleagues theoretically showed that the stationarity assumption may be avoided by estimating transfer entropy from an ensemble of realizations. Such an ensemble of realizations is often readily available in neuroscience experiments in the form of experimental trials. Thus, in this work we combine the ensemble method with a recently proposed transfer entropy estimator to make transfer entropy estimation applicable to non-stationary time series. We present an efficient implementation of the approach that is suitable for the increased computational demand of the ensemble method's practical application. In particular, we use a massively parallel implementation for a graphics processing unit to handle the computationally most heavy aspects of the ensemble method for transfer entropy estimation. We test the performance and robustness of our implementation on data from numerical simulations of stochastic processes. We also demonstrate the applicability of the ensemble method to magnetoencephalographic data. While we mainly evaluate the proposed method for neuroscience data, we expect it to be applicable in a variety of fields that are concerned with the analysis of information transfer in complex biological, social, and artificial systems.
Population Structure and Distribution Patterns of the Sibling Mosquito Species Culex pipiens and Culex torrentium (Diptera: Culicidae) Reveal Different Evolutionary Paths
Adriaan W. C. Dorresteijn
- Nowadays a number of endemic mosquito species are known to possess vector abilities for various diseases, as e.g. the sibling species Culex pipiens and Culex torrentium. Due to their morphological similarity, ecology, distribution and vector abilities, knowledge about these species' population structure is essential. Culicidae from 25 different sampling sites were collected from March till October 2012. All analyses were performed with aligned cox1 sequences with a total length of 658 bp. Population structure as well as distribution patterns of both species were analysed using molecular methods and different statistical tests like distance based redundancy analysis (dbDRA), analysis of molecular variances (AMOVA) or McDonald & Kreitman test and Tajima's D. Within both species, we could show a genetic variability among the cox1 fragment. The construction of haplotype networks revealed one dominating haplotype for Cx. pipiens, widely distributed within Germany and a more homogeneous pattern for Cx. torrentium. The low genetic differences within Cx. pipiens could be a result of an infection with Wolbachia which can induce a sweep through populations by passively taking the also maternally inherited mtDNA through the population, thereby reducing the mitochondrial diversity as an outcome of reproductive incompatibility. Pairwise population genetic differentiation (FST) ranged significantly from moderate to very great between populations of Cx. pipiens and Cx. torrentium. Analyses of molecular variances revealed for both species that the main genetic variability exists within the populations (Cx. pipiens [88.38%]; Cx. torrentium [66.54%]). Based on a distance based redundancy analysis geographical origin explained a small but significant part of the species' genetic variation. Overall, the results confirm that Cx. pipiens and Cx. torrentium underlie different factors regarding their mitochondrial differentiation, which could be a result of endosymbiosis, dispersal between nearly located populations or human introduction.
Prediction of the age at onset in spinocerebellar ataxia type 1, 2, 3 and 6
Sophie Tezenas du Montcel
Bart P. van de Warrenburg
Roberto Di Fabio
- Background The most common spinocerebellar ataxias (SCA)—SCA1, SCA2, SCA3, and SCA6—are caused by (CAG)n repeat expansion. While the number of repeats of the coding (CAG)n expansions is correlated with the age at onset, there are no appropriate models that include both affected and preclinical carriers allowing for the prediction of age at onset.
Methods We combined data from two major European cohorts of SCA1, SCA2, SCA3, and SCA6 mutation carriers: 1187 affected individuals from the EUROSCA registry and 123 preclinical individuals from the RISCA cohort. For each SCA genotype, a regression model was fitted using a log-normal distribution for age at onset with the repeat length of the alleles as covariates. From these models, we calculated expected age at onset from birth and conditionally that this age is greater than the current age.
Results For SCA2 and SCA3 genotypes, the expanded allele was a significant predictor of age at onset (−0.105±0.005 and −0.056±0.003) while for SCA1 and SCA6 genotypes both the size of the expanded and normal alleles were significant (expanded: −0.049±0.002 and −0.090±0.009, respectively; normal: +0.013±0.005 and −0.029±0.010, respectively). According to the model, we indicated the median values (90% critical region) and the expectancy (SD) of the predicted age at onset for each SCA genotype according to the CAG repeat size and current age.
Conclusions These estimations can be valuable in clinical and research. However, results need to be confirmed in other independent cohorts and in future longitudinal studies.
Aztec introduction of the great-tailed grackle in ancient Mesoamerica: Formal defense of the Sahaguntine historical account
Paul D. Haemig
- The historical account of Aztec Emperor Auitztol’s introduction of the great-tailed grackle Quiscalus mexicanus into the Valley of Mexico (1486–1502) is significant because it documents human translocation of wild birds in Mexico over 500 years ago, before the Spanish Conquest of that land. In the present paper, which defends the account from writings that dispute it, I first review the evidence of how the account was obtained and show that its many details are consistent with what is known from other sources about both the great-tailed grackle and the Aztecs (Nahuas). I then review and examine all published criticisms of the account and explain in detail why they are wrong. The critics have to date presented no persuasive evidence to support their speculation that the Aztecs confused, or might have confused, a natural invasion for an introduction. In contrast to these critics, Bernardino de Sahagún’s research group in the 1500s presented a highly credible, peer-reviewed historical account that documented Aztec introduction of the great-tailed grackle. The pioneering work of these Renaissance Mexican scholars continues to stand as one of the most important records of invasive alien species introduction in ancient times.
Invasion of yellow crazy ant Anoplolepis gracilipes in a Seychelles UNESCO palm forest
Christopher N. Kaiser-Bunbury
- The mature palm forest of the Vallée de Mai, a UNESCO World Heritage Site, on the Seychelles island of Praslin, is a unique ecosystem containing many endemic species, including the iconic coco de mer palm Lodoicea maldivica. In 2009, the invasive yellow crazy ant Anoplolepis gracilipes was recorded for the first time within the palm forest, raising concern about its potential impacts on the endemic fauna. This research aimed to: (1) assess the current distribution and spread of A. gracilipes within the palm forest; (2) identify environmental variables that are linked to A. gracilipes distribution; and (3) compare endemic species richness and abundance in A. gracilipes invaded and uninvaded areas. Anoplolepis gracilipes was confined to the north-east of the site and remained almost stationary between April 2010 and December 2012, with isolated outbreaks into the forest. Infested areas had significantly higher temperature and humidity and lower canopy cover. Abundance and species richness of the endemic arboreal fauna were lower in the A. gracilipes invaded area. Molluscs were absent from the invaded area. The current restricted distribution of A. gracilipes in this ecosystem, combined with lower abundance of endemic fauna in the invaded area, highlight the need for further research to assess control measures and the possible role of biotic resistance to the invasion of the palm forest by A. gracilipes.