Maternal inbreeding reduces parental care in the zebra finch, <i>Taeniopygia guttata</i>

Increased embryo mortality is the most commonly cited cause of reduced fitness in inbred organisms. Reduced embryo survival may be the result of reduced parental expenditure by inbred individuals and here we tested the hypothesis that inbreeding results in impaired incubation behaviour in captive zebra finches. We compared incubation attentiveness of inbred female zebra finches (derived from full-sibling mating) with that of control females (derived from unrelated parents) and found a statistically significant inbreeding depression of 17% in incubation attentiveness. This shows that inbreeding can significantly influence parental behaviour. Despite a reduction in the amount of time inbred females spent incubating, their partners were able to compensate for the reduced incubation attentiveness. Incubation temperature also did not differ between inbred and control females. To test for the effect of incubation behaviour, we fostered eggs laid by control females to either inbred or control females at the end of laying. Eggs that were incubated by inbred females had an 8.5% lower hatching success than eggs incubated by control females and, although based on a relatively small sample and not statistically significant, the magnitude of the difference was consistent with differences in hatching success observed in the wild under relatively benign environmental conditions. Thus, under more challenging environmental conditions usually encountered in the wild, the reduced incubation attentiveness of inbred females could provide one proximate explanation for the consistent finding of decreased hatching success with increasing maternal inbreeding in birds

Phase synchronization of coupled bursting neurons and the generalized Kuramoto model

Bursting neurons fire rapid sequences of action potential spikes followed by a quiescent period. The basic dynamical mechanism of bursting is the slow currents that modulate a fast spiking activity caused by rapid ionic currents. Minimal models of bursting neurons must include both effects. We considered one of these models and its relation with a generalized Kuramoto model, thanks to the definition of a geometrical phase for bursting and a corresponding frequency. We considered neuronal networks with different connection topologies and investigated the transition from a non-synchronized to a partially phase-synchronized state as the coupling strength is varied. The numerically determined critical coupling strength value for this transition to occur is compared with theoretical results valid for the generalized Kuramoto model.Comment: 31 pages, 5 figure

Universal dynamical properties preclude standard clustering in a large class of biochemical data

Motivation: Clustering of chemical and biochemical data based on observed features is a central cognitive step in the analysis of chemical substances, in particular in combinatorial chemistry, or of complex biochemical reaction networks. Often, for reasons unknown to the researcher, this step produces disappointing results. Once the sources of the problem are known, improved clustering methods might revitalize the statistical approach of compound and reaction search and analysis. Here, we present a generic mechanism that may be at the origin of many clustering difficulties. Results: The variety of dynamical behaviors that can be exhibited by complex biochemical reactions on variation of the system parameters are fundamental system fingerprints. In parameter space, shrimp-like or swallow-tail structures separate parameter sets that lead to stable periodic dynamical behavior from those leading to irregular behavior. We work out the genericity of this phenomenon and demonstrate novel examples for their occurrence in realistic models of biophysics. Although we elucidate the phenomenon by considering the emergence of periodicity in dependence on system parameters in a low-dimensional parameter space, the conclusions from our simple setting are shown to continue to be valid for features in a higher-dimensional feature space, as long as the feature-generating mechanism is not too extreme and the dimension of this space is not too high compared with the amount of available data. Availability and implementation: For online versions of super-paramagnetic clustering see http://stoop.ini.uzh.ch/research/clustering. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Bounds for the adiabatic approximation with applications to quantum computation

We present straightforward proofs of estimates used in the adiabatic approximation. The gap dependence is analyzed explicitly. We apply the result to interpolating Hamiltonians of interest in quantum computing.Comment: 15 pages, one figure. Two comments added in Secs. 2 and

Efficient visualization of high-throughput targeted proteomics experiments: TAPIR

Motivation: Targeted mass spectrometry comprises a set of powerful methods to obtain accurate and consistent protein quantification in complex samples. To fully exploit these techniques, a cross-platform and open-source software stack based on standardized data exchange formats is required. Results: We present TAPIR, a fast and efficient Python visualization software for chromatograms and peaks identified in targeted proteomics experiments. The input formats are open, community-driven standardized data formats (mzML for raw data storage and TraML encoding the hierarchical relationships between transitions, peptides and proteins). TAPIR is scalable to proteome-wide targeted proteomics studies (as enabled by SWATH-MS), allowing researchers to visualize high-throughput datasets. The framework integrates well with existing automated analysis pipelines and can be extended beyond targeted proteomics to other types of analyses. Availability and implementation: TAPIR is available for all computing platforms under the 3-clause BSD license at https://github.com/msproteomicstools/msproteomicstools. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Skin temperature reveals the intensity of acute stress

Acute stress triggers peripheral vasoconstriction, causing a rapid, short-term drop in skin temperature in homeotherms. We tested, for the first time, whether this response has the potential to quantify stress, by exhibiting proportionality with stressor intensity. We used established behavioural and hormonal markers: activity level and corticosterone level, to validate a mild and more severe form of an acute restraint stressor in hens (Gallus gallus domesticus). We then used infrared thermography (IRT) to non-invasively collect continuous temperature measurements following exposure to these two intensities of acute handling stress. In the comb and wattle, two skin regions with a known thermoregulatory role, stressor intensity predicted the extent of initial skin cooling, and also the occurrence of a more delayed skin warming, providing two opportunities to quantify stress. With the present, cost-effective availability of IRT technology, this non-invasive and continuous method of stress assessment in unrestrained animals has the potential to become common practice in pure and applied research

Proteomics studies confirm the presence of alternative protein isoforms on a large scale

Stably expressed alternatively-spliced protein isoforms are produced on a genome-wide scale in Drosophila

aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data

Motivation: The determination of absolute quantities of proteins in biological samples is necessary for multiple types of scientific inquiry. While relative quantification has been commonly used in proteomics, few proteomic datasets measuring absolute protein quantities have been reported to date. Various technologies have been applied using different types of input data, e.g. ion intensities or spectral counts, as well as different absolute normalization strategies. To date, a user-friendly and transparent software supporting large-scale absolute protein quantification has been lacking. Results: We present a bioinformatics tool, termed aLFQ, which supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/MS proteomics data, together with validation algorithms enabling automated data analysis and error estimation. Availability and implementation: aLFQ is written in R and freely available under the GPLv3 from CRAN (http://www.cran.r-project.org). Instructions and example data are provided in the R-package. The raw data can be obtained from the PeptideAtlas raw data repository (PASS00321). Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Quantum affine Cartan matrices, Poincare series of binary polyhedral groups, and reflection representations

We first review some invariant theoretic results about the finite subgroups of SU(2) in a quick algebraic way by using the McKay correspondence and quantum affine Cartan matrices. By the way it turns out that some parameters (a,b,h;p,q,r) that one usually associates with such a group and hence with a simply-laced Coxeter-Dynkin diagram have a meaningful definition for the non-simply-laced diagrams, too, and as a byproduct we extend Saito's formula for the determinant of the Cartan matrix to all cases. Returning to invariant theory we show that for each irreducible representation i of a binary tetrahedral, octahedral, or icosahedral group one can find a homomorphism into a finite complex reflection group whose defining reflection representation restricts to i.Comment: 19 page