The 10kTrees Website: A New Online Resource for Primate Phylogeny

The comparative method plays a central role in efforts to uncover the adaptive basis for primate behaviors, morphological traits, and cognitive abilities.[1-4] The comparative method has been used, for example, to infer that living in a larger group selects for a larger neocortex,[5][6] that primate territoriality favors a longer day range relative to home range size,[7] and that sperm competition can account for the evolution of primate testes size.[8][9] Comparison is fundamental for reconstructing behavioral traits in the fossil record, for example, in studies of locomotion and diet.[10-13] Recent advances in comparative methods require phylogenetic information,[2][14-16] but our knowledge of phylogenetic information is imperfect. In the face of uncertainty about evolutionary relationships, which phylogeny should one use? Here we provide a new resource for comparative studies of primates that enables users to run comparative analyses on multiple primate phylogenies Importantly, the 10,000 trees that we provide are not random, but instead use recent systematic methods to create a plausible set of topologies that reflect our certainty about some nodes on the tree and uncertainty about other nodes, given the dataset. The trees also reflect uncertainty about branch lengths.Human Evolutionary Biolog

Membrane penetration and trapping of an active particle

The interaction between nano- or micro-sized particles and cell membranes is of crucial importance in many biological and biomedical applications such as drug and gene delivery to cells and tissues. During their cellular uptake, the particles can pass through cell membranes via passive endocytosis or by active penetration to reach a target cellular compartment or organelle. In this manuscript, we develop a simple model to describe the interaction of a self-driven spherical particle (moving through an effective constant active force) with a minimal membrane system, allowing for both penetration and trapping. We numerically calculate the state diagram of this system, the membrane shape, and its dynamics. In this context, we show that the active particle may either get trapped near the membrane or penetrates through it, where the membrane can either be permanently destroyed or recover its initial shape by self-healing. Additionally, we systematically derive a continuum description allowing to accurately predict most of our results analytically. This analytical theory helps identifying the generic aspects of our model, suggesting that most of its ingredients should apply to a broad range of membranes, from simple model systems composed of magnetic microparticles to lipid bilayers. Our results might be useful to predict mechanical properties of synthetic minimal membranes.Comment: 16 pages, 6 figures. Revised manuscript resubmitted to J. Chem. Phy

Proteomic analysis of Daphnia magna hints at molecular pathways involved in defensive plastic responses

Background: Phenotypic plasticity in defensive traits occurs in many species when facing heterogeneous predator regimes. The waterflea Daphnia is well-known for showing a variety of these so called inducible defences. However, molecular mechanisms underlying this plasticity are poorly understood so far. We performed proteomic analysis on Daphniamagna exposed to chemical cues of the predator Triops cancriformis. D. magna develops an array of morphological changes in the presence of Triops including changes of carapace morphology and cuticle hardening. Results: Using the 2D-DIGE technique, 1500 protein spots could be matched and quantified. We discovered 179 protein spots with altered intensity when comparing Triops exposed animals to a control group, and 69 spots were identified using nano-LC MS/MS. Kairomone exposure increased the intensity of spots containing muscle proteins, cuticle proteins and chitin-modifying enzymes as well as enzymes of carbohydrate and energy metabolism. The yolk precursor protein vitellogenin decreased in abundance in 41 of 43 spots. Conclusion: Identified proteins may be either directly involved in carapace stability or reflect changes in energy demand and allocation costs in animals exposed to predator kairomones. Our results present promising candidate proteins involved in the expression of inducible defences in Daphnia and enable further in depth analysis of this phenomenon

Primate Extinction Risk and Historical Patterns of Speciation and Extinction in Relation to Body Mass

Body mass is thought to influence diversification rates, but previous studies have produced ambiguous results. We investigated patterns of diversification across 100 trees obtained from a new Bayesian inference of primate phylogeny that sampled trees in proportion to their posterior probabilities. First, we used simulations to assess the validity of previous studies that used linear models to investigate the links between IUCN Red List status and body mass. These analyses support the use of linear models for ordinal ranked data on threat status, and phylogenetic generalized linear models revealed a significant positive correlation between current extinction risk and body mass across our tree block. We then investigated historical patterns of speciation and extinction rates using a recently developed maximum-likelihood method. Specifically, we predicted that body mass correlates positively with extinction rate because larger bodied organisms reproduce more slowly, and body mass correlates negatively with speciation rate because smaller bodied organisms are better able to partition niche space. We failed to find evidence that extinction rates covary with body mass across primate phylogeny. Similarly, the speciation rate was generally unrelated to body mass, except in some tests that indicated an increase in the speciation rate with increasing body mass. Importantly, we discovered that our data violated a key assumption of sample randomness with respect to body mass. After correcting for this bias, we found no association between diversification rates and mass.Human Evolutionary Biolog

On the mixing property for a class of states of relativistic quantum fields

Let $\omega$ be a factor state on the quasi-local algebra $\cal{A}$ of observables generated by a relativistic quantum field, which in addition satisfies certain regularity conditions (satisfied by ground states and the recently constructed thermal states of the $P(\phi)_2$ theory). We prove that there exist space and time translation invariant states, some of which are arbitrarily close to $\omega$ in the weak* topology, for which the time evolution is weakly asymptotically abelian

LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: the Daphnia pulex genome database as a key for high throughput proteomics in Daphnia

<p>Abstract</p> <p>Background</p> <p>Daphniids, commonly known as waterfleas, serve as important model systems for ecology, evolution and the environmental sciences. The sequencing and annotation of the <it>Daphnia pulex </it>genome both open future avenues of research on this model organism. As proteomics is not only essential to our understanding of cell function, and is also a powerful validation tool for predicted genes in genome annotation projects, a first proteomic dataset is presented in this article.</p> <p>Results</p> <p>A comprehensive set of 701,274 peptide tandem-mass-spectra, derived from <it>Daphnia pulex</it>, was generated, which lead to the identification of 531 proteins. To measure the impact of the <it>Daphnia pulex </it>filtered models database for mass spectrometry based <it>Daphnia </it>protein identification, this result was compared with results obtained with the Swiss-Prot and the <it>Drosophila melanogaster </it>database. To further validate the utility of the <it>Daphnia pulex </it>database for research on other <it>Daphnia </it>species, additional 407,778 peptide tandem-mass-spectra, obtained from <it>Daphnia longicephala</it>, were generated and evaluated, leading to the identification of 317 proteins.</p> <p>Conclusion</p> <p>Peptides identified in our approach provide the first experimental evidence for the translation of a broad variety of predicted coding regions within the <it>Daphnia </it>genome. Furthermore it could be demonstrated that identification of <it>Daphnia longicephala </it>proteins using the <it>Daphnia pulex </it>protein database is feasible but shows a slightly reduced identification rate. Data provided in this article clearly demonstrates that the <it>Daphnia </it>genome database is the key for mass spectrometry based high throughput proteomics in <it>Daphnia</it>.</p

Random fluctuation leads to forbidden escape of particles

A great number of physical processes are described within the context of Hamiltonian scattering. Previous studies have rather been focused on trajectories starting outside invariant structures, since the ones starting inside are expected to stay trapped there forever. This is true though only for the deterministic case. We show however that, under finitely small random fluctuations of the field, trajectories starting inside Arnold-Kolmogorov-Moser (KAM) islands escape within finite time. The non-hyperbolic dynamics gains then hyperbolic characteristics due to the effect of the random perturbed field. As a consequence, trajectories which are started inside KAM curves escape with hyperbolic-like time decay distribution, and the fractal dimension of a set of particles that remain in the scattering region approaches that for hyperbolic systems. We show a universal quadratic power law relating the exponential decay to the amplitude of noise. We present a random walk model to relate this distribution to the amplitude of noise, and investigate this phenomena with a numerical study applying random maps.Comment: 6 pages, 6 figures - Up to date with corrections suggested by referee

Enhancing Oxygen Uptake Efficiency Through Nasal Breathing in Aerobic Exercise

An individual’s ability to use oxygen to sustain aerobic performance, as denoted by the oxygen uptake efficiency (OUE), is calculated by dividing oxygen uptake (VO2) by ventilation (VE). Whether nasal breathing (NB) during exercise would improve OUE more significantly compared to combined breathing (CB) remains uncertain. PURPOSE: To determine the effects of utilizing NB during exercise on OUE. METHODS: Fourteen males (age: 20.57 ± 1.22 yrs; BMI: 26.03 ± 3.16 kg/m2) were randomly assigned to the NB (n = 8) or CB (n = 6) group for a 4-week supervised aerobic exercise intervention conducted four times per week for 30 minutes at moderate intensity (70% maximal heart rate). VO2max tests were performed during the pre- (week 0) and post-study (week 4) periods on a recumbent bike to determine the change in OUE, VO2, and VE at varying intensities (40%, 55%, 70%, 85%, and 100% of VO2max). The OUE was calculated as VO2 (L) ÷ VE (L). A one-way ANCOVA, controlling for OUE, VO2, and VE at pre-study, was utilized to examine if NB elicited cardiorespiratory adaptations that were superior to the CB training at post-study. A paired-sample t-test examined changes in OUE, VO2, and VE throughout the GXT from week 0 to week 4. Data are presented as mean ± standard error. RESULTS: The NB group demonstrated significantly greater [F(1,11) = 7.213, p = 0.021] OUE (0.048 ± 0.002) at 85% of VO2max than the CB (0.037 ± 0.003) group. Similarly, the NB group had a significantly greater (p = 0.014) OUE (0.025 ± 0.001) at 100% of VO2max than the CB (0.021 ± 0.001) group. Only the NB group experienced significant improvements after exercise training in VO2 at 40% ( p = 0.003, 12.02 ± 0.50 to 13.72 ± 0.59 mL·kg·min-1], 55% (p = 0.006, 16.68 ± 0.71 to 18.87 ± 0.81 mL·kg·min-1), 70% (p = 0.005, 21.16 ± 0.93 to 24.00 ± 1.01 mL·kg·min-1), 85% (p = 0.004, 25.81 ± 1.11 to 29.03 ± 1.23 mL·kg·min-1), and 100% VO2max (p = 0.005, 30.31 ± 1.30 to 34.18 ± 1.48 mL·kg·min-1). While not statistically significant, the NB group displayed a trend of reduced VE compared to the CB group. CONCLUSION: The integration of NB during aerobic exercise enhanced the OUE, particularly at higher intensities, compared to CB. This adaptation is noteworthy, as the NB group achieved a comparable range of VO2 as the CB group while maintaining a lower VE after just 1-month of training. This denotes that NB could promote enhanced oxygen movement. Future studies are warranted to investigate additional health adaptations resulting from such training benefits