Truncated power laws: a tool for understanding aggregation patterns in animals?

Statistical distributions like the negative binomial distribution are commonly used to describe aggregation patterns in animals. However, recently it has been suggested that truncated power laws (TPLs) may also be used for this kind of analysis. A TPL consists of two power functions separated by a cut-off size ( C *). The cut-off size and the slope of power function one (β₁) for the smallest group sizes have been suggested to have a biological explanatory value.
We applied TPLs to aggregation data of tephritid seed predators on a composite plant, aphids on willows and grey seals on a haulout site. β₁ varied between 0.60 and and −0.72, which is higher than predicted. In addition, resource distribution and animal density influenced β₁ and C *. This indicates that environmental dimensionality suggested to affect β₁ is masked by ecological factors. We conclude that TPLs are useful due to their simplicity and, in comparison with traditional methods, provide additional biologically relevant information. Truncated power laws can therefore prove to be useful in studies of animal behaviour and population dynamics.     

Oxidoreductases that Act as Conditional Virulence Suppressors in Salmonella enterica Serovar Typhimurium

In Salmonella enterica serovar Typhimurium, oxidoreductases of the thioredoxin superfamily contribute to bacterial invasiveness, intracellular replication and to the virulence in BALB/c mice as well as in the soil nematode Caenorhabditis elegans. The scsABCD gene cluster, present in many but not all enteric bacteria, codes for four putative oxidoreductases of the thioredoxin superfamily. Here we have analyzed the potential role of the scs genes in oxidative stress tolerance and virulence in S. Typhimurium. An scsABCD deletion mutant showed moderate sensitization to the redox-active transition metal ion copper and increased protein carbonylation upon exposure to hydrogen peroxide. Still, the scsABCD mutant was not significantly affected for invasiveness or intracellular replication in respectively cultured epithelial or macrophage-like cells. However, we noted a significant copper chloride sensitivity of SPI1 T3SS mediated invasiveness that strongly depended on the presence of the scs genes. The scsABCD deletion mutant was not attenuated in animal infection models. In contrast, the mutant showed a moderate increase in its competitive index upon intraperitoneal challenge and enhanced invasiveness in small intestinal ileal loops of BALB/c mice. Moreover, deletion of the scsABCD genes restored the invasiveness of a trxA mutant in epithelial cells and its virulence in C. elegans. Our findings thus demonstrate that the scs gene cluster conditionally affects virulence and underscore the complex interactions between oxidoreductases of the thioredoxin superfamily in maintaining host adaptation of S. Typhimurium.     

Convergence in the distribution patterns of Europe’s plants and mammals is due to environmental forcing

Aim Our aims were to test: (1) the extent to which vascular plant associations are related in space to mammalian associations, and (2) whether the plant associations are more closely related than the mammalian associations to climate and to a published environmental stratification of Europe. Location Europe, as defined by the following boundaries: 11° W, 32° E, 71° N and 35° N. Methods The analysis is based on presence/absence records of mammal species and plant species with a resolution of 50 km × 50 km. The similarity of the overall spatial structure was tested using a partial Mantel test while controlling for the effect of geographical proximity. To further identify the main spatial components in the datasets, we used k‐means clustering and principal components analysis. The resulting geographical patterns were compared with one another, with climate variables and with the environmental stratification of Europe. Results The clustering of the plant data forms coherent areas that can be interpreted as reflections of floristic regions that are controlled to a large extent by climate and topography. In terms of the correlation between distance matrices, the relationship between plants and mammals is relatively strong. The relationships between mammals and climate, and between plants and climate, are more complex but always statistically significant. There is no evidence that the plant clusters are more closely related than the mammalian clusters to climate, although plant clusters are closer to environmental data than to climate. Main conclusions The clustering patterns of mammals and plants form groups that agree with one another in their spatial extent. The forcing of floristic patterns into coherent entities appears mainly to be caused by climatic variables (temperature, temperature range and rainfall), mediated by elevation differences. The formation of individual plant clusters is also related to species numbers and to local and regional floristic differences. The close correlation between the floristic and faunal patterns suggests that the mammal and plant distributions are controlled by the same environmental variables, although the extent to which the mammals are controlled directly by climate or through the influence of vegetation requires more detailed study.     

Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures

Background  

The structure of proteins may change as a result of the inherent flexibility of some protein regions. We develop and explore probabilistic machine learning methods for predicting a continuum secondary structure, i.e. assigning probabilities to the conformational states of a residue. We train our methods using data derived from high-quality NMR models.     

FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations

Near linear scaling fragment based quantum chemical calculations are becoming increasingly popular for treating large systems with high accuracy and is an active field of research. However, it remains difficult to set up these calculations without expert knowledge. To facilitate the use of such methods, software tools need to be available to support these methods and help to set up reasonable input files which will lower the barrier of entry for usage by non-experts. Previous tools relies on specific annotations in structure files for automatic and successful fragmentation such as residues in PDB files. We present a general fragmentation methodology and accompanying tools called FragIt to help setup these calculations. FragIt uses the SMARTS language to locate chemically appropriate fragments in large structures and is applicable to fragmentation of any molecular system given suitable SMARTS patterns. We present SMARTS patterns of fragmentation for proteins, DNA and polysaccharides, specifically for D-galactopyranose for use in cyclodextrins. FragIt is used to prepare input files for the Fragment Molecular Orbital method in the GAMESS program package, but can be extended to other computational methods easily.     

Fms-Like Tyrosine Kinase 3 Ligand Controls Formation of Regulatory T Cells in Autoimmune Arthritis

Fms-like tyrosine kinase 3 ligand (Flt3L) is known as the primary differentiation and survival factor for dendritic cells (DCs). Furthermore, Flt3L is involved in the homeostatic feedback loop between DCs and regulatory T cell (Treg). We have previously shown that Flt3L accumulates in the synovial fluid in rheumatoid arthritis (RA) and that local exposure to Flt3L aggravates arthritis in mice, suggesting a possible involvement in RA pathogenesis. In the present study we investigated the role of Flt3L on DC populations, Tregs as well as inflammatory responses in experimental antigen-induced arthritis. Arthritis was induced in mBSA-immunized mice by local knee injection of mBSA and Flt3L was provided by daily intraperitoneal injections. Flow cytometry analysis of spleen and lymph nodes revealed an increased formation of DCs and subsequently Tregs in mice treated with Flt3L. Flt3L-treatment was also associated with a reduced production of mBSA specific antibodies and reduced levels of the pro-inflammatory cytokines IL-6 and TNF-α. Morphological evaluation of mBSA injected joints revealed reduced joint destruction in Flt3L treated mice. The role of DCs in mBSA arthritis was further challenged in an adoptive transfer experiment. Transfer of DCs in combination with T-cells from mBSA immunized mice, predisposed naïve recipients for arthritis and production of mBSA specific antibodies. We provide experimental evidence that Flt3L has potent immunoregulatory properties. Flt3L facilitates formation of Treg cells and by this mechanism reduces severity of antigen-induced arthritis in mice. We suggest that high systemic levels of Flt3L have potential to modulate autoreactivity and autoimmunity.     

Taxon names as paradigms: the structure of nomenclatural revolutions

In the present paper I argue that the two systems of phylogenetic nomenclature hitherto proposed represent, in a generalized sense, two different philosophies for how science develops and progresses. The phylogenetic system of definition initially proposed by de Queiroz and Gauthier [Syst. Zool. 39 (1990) 307], and later labeled PSD, is typically Popperian in the sense that science progresses toward truth by an accumulation of knowledge. Phylogenetic definitions of taxon names are assumed to adapt automatically to each new hypothesis of phylogeny, thereby reflecting better and better hypotheses. The phylogenetic system of reference proposed by Härlin [Zool. Scr. 27 (1998a) 381], on the other hand, is more Kuhnian, because it is built on the idea that successive hypotheses are incommensurable (and thus not cumulative) and that taxon names might be equalled with low‐level paradigms.     

Competitive Binding Between Unmodified and Etheno DNA Provides Information About Structure and Stoichiometry of RECA-DNA Complexes

Abstract

RecA is found to form three different complexes with single-stranded DNA with stoichiometries of 3, 6, and  9 nucleotides per RecA monomer. In the first two complexes the DNA bases are oriented preferentially perpendicular to the fiber axis of the complex. The second complex is shown to involve two different DNA strands.