Salix bifax undS. Mariana

Ohne Zusammenfassung     

Using variation partitioning techniques to quantify the effects of invasive alien species on native urban bird assemblages

Quantifying the impacts that invasive alien species (IAS) cause on affected systems is not an easy task. Here, we explore the application of variation partitioning techniques to measure and control for the effects of possible confounding factors when studying the impact that feral pigeons, European starlings, and house sparrows cause on native urban bird communities in Mexico. We argue that these IAS are provoking a severe impact on whole assemblages of native passerines only if (a) their marginal effect is statistically significant, (b) it remains so after partialling out other explanatory variables, and (c) is larger than (or similar to) the conditional effect of these covariates. We censused passerine bird assemblages and measured habitat variables in a number of greenspaces in three replicate study areas. Then, by means of partial redundancy analyses, we decomposed the total variability in bird data as a function of IAS, physical variables and vegetation data. In one of the study areas the marginal effect of IAS on native assemblages was significant, but the conditional effect was not. We conclude that this IAS effect was confounded with other explanatory variables. In the other study areas, no (marginal or partial) significant effect was found. Without invoking interspecific competition, our results support the opportunistic hypothesis, according to which IAS can exploit ecological conditions in modern cities that native species cannot even tolerate. Finally, apart from the Precautionary Principle, we found no scientific justification to control the abundance of the three IAS in our study areas.     

IGFs and IGF-Binding Proteins in the Synovial Fluid of Patients with Rheumatoid Arthritis and Osteoarthritis

International Journal of Peptide Research and Therapeutics - The progressive damage of human articular cartilage is associated with loss of integrity of its extracellular matrix components. Their...     

Compositional turnover and variation in Eemian pollen sequences in Europe

Vegetation History and Archaeobotany - The Eemian interglacial represents a natural experiment on how past vegetation with negligible human impact responded to amplified temperature changes...     

One size does not fit all: Customizing MCMC methods for hierarchical models using NIMBLE

Improved efficiency of Markov chain Monte Carlo facilitates all aspects of statistical analysis with Bayesian hierarchical models. Identifying strategies to improve MCMC performance is becoming increasingly crucial as the complexity of models, and the run times to fit them, increases. We evaluate different strategies for improving MCMC efficiency using the open‐source software NIMBLE (R package nimble) using common ecological models of species occurrence and abundance as examples. We ask how MCMC efficiency depends on model formulation, model size, data, and sampling strategy. For multiseason and/or multispecies occupancy models and for N‐mixture models, we compare the efficiency of sampling discrete latent states vs. integrating over them, including more vs. fewer hierarchical model components, and univariate vs. block‐sampling methods. We include the common MCMC tool JAGS in comparisons. For simple models, there is little practical difference between computational approaches. As model complexity increases, there are strong interactions between model formulation and sampling strategy on MCMC efficiency. There is no one‐size‐fits‐all best strategy, but rather problem‐specific best strategies related to model structure and type. In all but the simplest cases, NIMBLE's default or customized performance achieves much higher efficiency than JAGS. In the two most complex examples, NIMBLE was 10–12 times more efficient than JAGS. We find NIMBLE is a valuable tool for many ecologists utilizing Bayesian inference, particularly for complex models where JAGS is prohibitively slow. Our results highlight the need for more guidelines and customizable approaches to fit hierarchical models to ensure practitioners can make the most of occupancy and other hierarchical models. By implementing model‐generic MCMC procedures in open‐source software, including the NIMBLE extensions for integrating over latent states (implemented in the R package nimbleEcology), we have made progress toward this aim.     

Detection of Borrelia burgdorferi s.l., Anaplasma phagocytophilum and Babesia spp. in Dermacentor reticulatus ticks found within the city of Białystok,Poland—first data

Pathogens carried by ticks pose a threat to both human and animal health across the world. Typically associated with rural landscapes, ticks appear to adapt well to life in urban recreational areas. Although Dermacentor reticulatus is commonly found across Europe, data on the prevalence of pathogens in this tick species, in an urban environment, are very limited. PCR was used to examine 368 D. reticulatus individuals collected in the Zwierzyniecki Forest Nature Reserve in Bia?ystok, Poland. In total, 10.3% of ticks were infected, with Babesia spp. (9.2%), Anaplasma phagocytophilum (0.8%) and Borrelia burgdorferi sensu lato (0.3%). Rickettsia spp., Bartonella spp., and Coxiella burnetii were not detected. Sequence analysis for Babesia-positive samples identified 79.4% of them as Babesia canis, 8.8% as Babesia microti, 5.9% as Babesia spp., 2.9% as Babesia venatorum, and 2.9% as Babesia vogeli. Results obtained in this study indicate that D. reticulatus ticks found within the urban premises of the study area are infected with at least three pathogens and therefore are an important factor in public health risk for tick-borne diseases.

     

The Codon Usage in the Minimal Natural Cell

A statistical analysis of the variation in contents with the size of the current known smallest genomes, N. deltocephalinicola, C. ruddii, N. equitans, and M. genitalium, enabled the indication of a minimal set of codons capable of naturally building a modern-type free-living unicellular organism in an early stage of evolution. Using a linear regression model, the potential codon distribution in the minimal natural cell was predicted and compared to the composition of the smallest synthetic, JCVI-Syn3.0. The distribution of the molecular weight of potentially coded amino acids was also calculated. The main differences in the features of the minimal natural cell and H. Sapiens genome were analyzed. In this regard, the content percentage of respective amino acids and their polarization charge properties were reported and compared. The fractions of occurring nucleotides were calculated, too. Then, the estimated numbers of codons in a minimal natural cell were related to the expected numbers for random distribution. Shown increase, or decrease in the contents, relative to the calculated random filling was related to the evolutionary preferences, varying with the subsequent eras of the evolution of genetic code.

     

The development and characterization of an E. coli O25B bioconjugate vaccine

Extraintestinal pathogenic Escherichia coli (ExPEC) cause a wide range of clinical diseases such as bacteremia and urinary tract infections. The increase of multidrug resistant ExPEC strains is becoming a major concern for the treatment of these infections and E. coli has been identified as a critical priority pathogen by the WHO. Therefore, the development of vaccines has become increasingly important, with the surface lipopolysaccharide constituting a promising vaccine target. This study presents genetic and structural analysis of clinical urine isolates from Switzerland belonging to the serotype O25. Approximately 75% of these isolates were shown to correspond to the substructure O25B only recently described in an emerging clone of E. coli sequence type 131. To address the high occurrence of O25B in clinical isolates, an O25B glycoconjugate vaccine was prepared using an E. coli glycosylation system. The O antigen cluster was integrated into the genome of E. coli W3110, thereby generating an E. coli strain able to synthesize the O25B polysaccharide on a carrier lipid. The polysaccharide was enzymatically conjugated to specific asparagine side chains of the carrier protein exotoxin A (EPA) of Pseudomonas aeruginosa by the PglB oligosaccharyltransferase from Campylobacter jejuni. Detailed characterization of the O25B-EPA conjugate by use of physicochemical methods including NMR and GC-MS confirmed the O25B polysaccharide structure in the conjugate, opening up the possibility to develop a multivalent E. coli conjugate vaccine containing O25B-EPA.