Calcium regulation of mitochondria motility and morphology

In the Fifties, electron microscopy studies on neuronal cells showed that mitochondria typically cluster at synaptic terminals, thereby introducing the concept that proper mitochondria trafficking and partitioning inside the cell could provide functional support to the execution of key physiological processes. Today, the notion that a central event in the life of every eukaryotic cell is to configure, maintain, and reorganize the mitochondrial network at sites of high energy demand in response to environmental and cellular cues is well established, and the challenge ahead is to define the underlying molecular mechanisms and regulatory pathways. Recent pioneering studies have further contributed to place mitochondria at the center of the cell biology by showing that the machinery governing remodeling of mitochondria shape and structure regulates the functional output of the organelle as the powerhouse of the cell, the gateway to programmed cell death, and the platform for Ca²⁺ signaling. Thus, a raising issue is to identify the cues integrating mitochondria trafficking and dynamics into cell physiology and metabolism. Given the versatile function of calcium as a second messenger and of the role of mitochondria as a major calcium store, evidences are emerging linking Ca²⁺ transients to the modulation of mitochondrial activities. This review focuses on calcium as a switch controlling mitochondria motility and morphology in steady state, stressed, and pathological conditions.     

Dynamical structure of transfer RNA studied by normal mode analysis

The internal motion of yeast phenylalanine transfer RNA is studied by normal mode analysis in extended dihedral angle space, in which the flexibility of five-membered ribose rings is treated faithfully by introducing a variable for its pseudo-rotational motion. Analysis of global molecular motions reveals that the molecule is very soft. We show that this softness comes not from the property of the “material” comprising the molecule but from its slender shape. Analysis of thermal distance fluctuations reveals that this molecule can be regarded as consisting dynamically of three blocks. Thermal fluctuations of the mainchain dihedral angles show rigidity of the anticodon region. They also show flexibility of regions around nonstacking bases. Base-stacking interactions cause suppression of the correlated functions of mainchain dihedral angles beyond a ribose ring. We analyze the thermal fluctuation of parameters describing the positions of two adjacent bases. Fluctuations of relative translational parameters in the anticodon and acceptor stem regions are found to be larger than those in other stem regions. The relative translational motions cause the two stem regions to undergo global twisting and bending motions. We show that the role of pseudo-rotational motion of sugars is important in regions around bases which are involved in nonregular interactions. Received: 29 October 1998 / Revised version: 8 February 1999 / Accepted: 11 February 1999     

Predicting to new environments: tools for visualizing model behaviour and impacts on mapped distributions

Data limitations can lead to unrealistic fits of predictive species distribution models (SDMs) and spurious extrapolation to novel environments. Here, we want to draw attention to novel combinations of environmental predictors that are within the sampled range of individual predictors but are nevertheless outside the sample space. These tend to be overlooked when visualizing model behaviour. They may be a cause of differing model transferability and environmental change predictions between methods, a problem described in some studies but generally not well understood. We here use a simple simulated data example to illustrate the problem and provide new and complementary visualization techniques to explore model behaviour and predictions to novel environments. We then apply these in a more complex real‐world example. Our results underscore the necessity of scrutinizing model fits, ecological theory and environmental novelty.     

Separating the impact of group size, density, and enclosure size on broiler movement and space use at a decreasing perimeter to area ratio

The goal of this study was to determine the impact of enclosure size on space use and movement patterns of domestic fowl (Gallus gallus domesticus), independent of group size and density. Research designed to estimate the effects of group size, density, or enclosure size involves inherent confounding between factors, clouding their individual effects. This experimental design enabled us to conduct multiple contrasts in order to tease apart the specific impacts. Treatments consisted of five combinations of three square enclosures: small (S; 1.5 m²), medium (M; 3.0 m²), and large (L; 4.5 m²), and three group sizes of 10, 20, and 30 birds. We made comparisons while holding group size constant, holding density constant, and the third while maintaining a constant enclosure size. Nearest neighbor distances increased with enclosure size but appeared to be constrained by density. Net displacement and minimum convex polygons increased with enclosure size regardless of group size or density. We found no evidence of social restriction on space use. Results indicate that broilers adapted their use of space and movement patterns to the size of the enclosures, spreading out and utilizing a greater amount of space when it was available.     

Regulation of mitochondrial phospholipids by Ups1/PRELI-like proteins depends on proteolysis and Mdm35

The mitochondrial phospholipid metabolism critically depends on members of the conserved Ups1/PRELI‐like protein family in the intermembrane space. Ups1 and Ups2 (also termed Gep1) were shown to regulate the accumulation of cardiolipin (CL) and phosphatidylethanolamine (PE), respectively, in a lipid‐specific but coordinated manner. It remained enigmatic, however, how the relative abundance of both phospholipids in mitochondrial membranes is adjusted on the molecular level. Here, we describe a novel regulatory circuit determining the accumulation of Ups1 and Ups2 in the intermembrane space. Ups1 and Ups2 are intrinsically unstable proteins, which are degraded by distinct mitochondrial peptidases. The turnover of Ups2 is mediated by the i‐AAA protease Yme1, whereas Ups1 is degraded by both Yme1 and the metallopeptidase Atp23. We identified Mdm35, a member of the twin Cx₉C protein family, as a novel interaction partner of Ups1 and Ups2. Binding to Mdm35 ensures import and protects both proteins against proteolysis. Homologues to all components of this pathway are present in higher eukaryotes, suggesting that the regulation of mitochondrial CL and PE levels is conserved in evolution.     

The home-range concept: are traditional estimators still relevant with modern telemetry technology?

Recent advances in animal tracking and telemetry technology have allowed the collection of location data at an ever-increasing rate and accuracy, and these advances have been accompanied by the development of new methods of data analysis for portraying space use, home ranges and utilization distributions. New statistical approaches include data-intensive techniques such as kriging and nonlinear generalized regression models for habitat use. In addition, mechanistic home-range models, derived from models of animal movement behaviour, promise to offer new insights into how home ranges emerge as the result of specific patterns of movements by individuals in response to their environment. Traditional methods such as kernel density estimators are likely to remain popular because of their ease of use. Large datasets make it possible to apply these methods over relatively short periods of time such as weeks or months, and these estimates may be analysed using mixed effects models, offering another approach to studying temporal variation in space-use patterns. Although new technologies open new avenues in ecological research, our knowledge of why animals use space in the ways we observe will only advance by researchers using these new technologies and asking new and innovative questions about the empirical patterns they observe.     

Recovery of understorey vegetation after release from a long history of sheep grazing in a herb‐rich woodland

The effects of stock grazing on native grassy ecosystems in temperate southern Australia are well documented. However, less is known about the potential of ecosystems to recover after a long history of stock grazing and, in particular, whether the removal of stock will have positive, negative or neutral impacts on biodiversity. We examined the response of understorey vegetation to the removal of sheep grazing in a herb‐rich Eucalyptus camaldulensis (red gum) woodland in western Victoria. Using a space‐for‐time chronosequence, woodlands were stratified into groups based on their time‐since‐grazing removal; these were long‐ungrazed (>20 years), intermediate‐time‐since‐grazing (9–14 years), recently ungrazed (5 years) and continuously grazed. We found significantly higher species density in long‐ungrazed sites relative to sites with a more recent grazing history. No differences were found in species density between continuously grazed sites and those ungrazed in the previous 14 years. Species composition differed with time‐since‐grazing removal and indicator species analysis detected several native species (including tall native geophytes and herbs) associated with long‐ungrazed sites that were absent or in low abundance in the more recently grazed sites. Seven of the eight species significantly associated with continuously grazed sites were exotic. Removal of sheep grazing in red gum woodlands can have positive benefits for understorey diversity but it is likely that recovery of key indicators such as native species will be slow.     

Chaotic based reconstructed phase space features for detecting ventricular fibrillation

Among the variety of cardiac arrhythmias, ventricular fibrillation (VF) and ventricular tachycardia (VT) are life-threatening; thus, accurate classification of these arrhythmias is a crucial task for cardiologists. Nevertheless, VT and VF signals are very similar in the time domain and accurate distinguishing these signals with naked eyes in some cases is impossible. In this paper, a novel self-similarity image-based scheme is introduced to classify the underlying information of VT, VF and normal electrocardiogram (ECG) signals. In this study, VT, VF and normal ECG signals are selected from CCU of the Royal Infirmary of Edinburgh and MIT-BIH datasets. According to the time delay method, signal samples can be assigned to state variables and a trajectory can be achieved. To extract the proposed self-similarity feature, first, two different trajectories from each signal trial are drawn according to two different delay time values. The two-dimensional state space of each trial trajectory is considered as an image. Therefore, two trajectory images are produced for each signal. Number of visited pixels in the first image is determined and is subtracted from that of the second image as the self-similarity feature of that signal. Moreover, another scheme is proposed to have a better estimation of self-similarity in which the logical AND operator is applied to both images (matrices) of each ECG trial. The third proposed criterion is similar to box counting method by this difference that each pixel is assigned a weight according to the trajectory density at that point and finally visited weighted pixels are counted. To classify VF from VT and normal ECG, a threshold is determined through the cross validation phase under the Receiver Operating Characteristic (ROC) criterion. To assess the proposed methods, the mentioned signals are classified using the-state-of-art chaotic features such as correlation dimension, the largest Lyapunov exponent and Approximate Entropy (ApEn). Experimental results indicate superiority of the proposed method in classifying the VT, VF and normal ECG signals compared to present traditional schemes. In addition, computational complexity of the introduced methods is very low and can be implemented in real-time applications.     

Partitioning of habitable pore space in earthworm burrows

Earthworms affect macro-pore structure of soils. However, some studies suggest that earthworm burrow walls and casts themselves differ greatly in structure from surrounding soils, potentially creating habitat for microbivorours nematodes which accelerate the decomposition and C and N mineralization. In this study aggregates were sampled from the burrow walls of the anecic earthworm Lumbricus terrestris and bulk soil (not altered by earthworms) from mesocosm incubated in the lab for 0, 1, 3, 5 and 16 weeks. Pore volumes and pore sizes were measured in triplicate with Mercury Intrusion Porosimetry (MIP). This method is well suited to establish pore size structure in the context of habitat, because it measures the stepwise intrusion of mercury from the outside of the aggregate into ever smaller pores. The progress of mercury into the aggregate interior thus resembles potential paths of a nematode into accessible habitable pore spaces residing in an aggregate. Total specific pore volume, V(s), varied between 0.13 and 0.18 mL/g and increased from 3 to 16 weeks in both burrow and bulk soil. Differences between total V(s) of bulk and burrow samples were not significant on any sampling date. However, differences were significant for pore size fractions at the scale of nematode body diameter.     

Modeling the Role of Diffusion Coefficients on Turing Instability in a Reaction-diffusion Prey-predator System

The paper is concerned with the effect of variable dispersal rates on Turing instability of a non-Lotka-Volterra reaction-diffusion system. In ecological applications, the dispersal rates of different species tends to oscillate in time. This oscillation is modeled by temporal variation in the diffusion coefficient with large as well as small periodicity. The case of large periodicity is analyzed using the theory of Floquet multipliers and that of the small periodicity by using Hill's equation. The effect of such variation on the resulting Turing space is studied. A comparative analysis of the Turing spaces with constant diffusivity and variable diffusivities is performed. Numerical simulations are carried out to support analytical findings.