Regional and local patterns in plant species richness with respect to resource availability

The hump-shaped relationship between plant species richness and productivity is a well-established and important paradigm. While plot-based species richness patterns on local scales have received much attention, little is currently known about species-based patterns on a regional scale. Using Ellenberg's indicator values for 1802 plant species in central Europe, we assess the patterns in regional species richness with respect to light, water, and mineral nutrient availability – three variables that strongly influence productivity. The results of this analysis are compared to those of published studies on smaller scales leading to the following conclusions:

• 1.

  On a regional scale in central Europe there is a hump-shaped relationship between soil nutrient supply and plant species richness within a given biome.

       
  
  

Contributions of heart rate and contractility to myocardial oxygen balance during exercise

The respective contributions of heart rate (HR) reduction and left ventricular (LV) negative inotropy to the effects of antianginal drugs are debated. Accordingly, eight instrumented dogs were investigated during exercise at spontaneous and paced HR (250 beats/min) after administration of either saline, atenolol, or ivabradine (selective pacemaker current channel blocker). During exercise, atenolol and ivabradine (both 1 mg/kg iv) similarly reduced HR (-30% from 222 +/- 5 beats/min), and LV mean ejection wall stress was not altered. LV dP/dt(max) was reduced by atenolol but not ivabradine. Diastolic time (DT) was increased by atenolol versus saline (195 +/- 6 vs. 123 +/- 4 ms, respectively) and to a greater extent by ivabradine (233 +/- 11 ms). Myocardial oxygen consumption (MVo(2)) was lower under ivabradine and atenolol versus saline (6.7 +/- 0.6 and 4.7 +/- 0.4 vs. 8.1 +/- 0.6 ml/min, respectively, P < 0.05). Under pacing, DT and MVo(2) were similar between ivabradine and saline but significantly reduced with atenolol. Thus HR reduction and negative inotropy equally contribute to the reduction in MVo(2) during exercise in the normal heart. The negative inotropy limits the increase in DT afforded by HR reduction.     

Similar patterns of local barn owl adaptation in the Middle East and Europe with respect to melanic coloration

The maintenance of phenotypic variation is a central question in evolutionary biology. A commonly suggested mechanism is that of local adaptation, whereby different phenotypes are adapted to alternative environmental conditions. A recent study in the European barn owl (Tyto alba) has shown that natural selection maintains a strong clinal variation in reddish pheomelanin‐based coloration. Studies in the region where phenotypic variation in this owl is the highest in Europe have further demonstrated that dark‐reddish and pale‐reddish owls exploit open and wooded habitats, predate voles and wood mice, and are long‐tailed and short‐tailed, respectively. However, it remains unclear as to whether these traits evolved as a consequence of allopatric evolution of dark colour in northern Europe and white colour in southern Europe, during which owls could have also evolved different morphologies and foraging behaviour. This scenario implies that covariation between coloration and foraging behaviour could be a specificity of the European continent, which is not found in other worldwide‐distributed populations. To investigate this issue, we studied a barn owl population in the Middle East. The results obtained show that, as in Central Europe, dark‐reddish female owls breed more often in the open landscape than their pale‐reddish female conspecifics, their offspring are fed with more voles than Muridae, and they are longer‐winged and longer‐tailed. These findings indicate that, in the barn owl, the association in females between pheomelanin‐based coloration and foraging behaviour and morphology is not restricted to the European continent but may well evolve in sympatry in many barn owl populations worldwide. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 447–454.     

Inflammatory mediators and the failing heart: a translational approach

Recent studies have identified the importance of proinflammatory mediators in regulating cardiac structure in health and disease. Recent studies suggest that cytokines that are expressed within the myocardium in response to a environmental injury, namely tumor necrosis factor-alpha (TNF), interleukin-1 (IL-1) and the interleukin-6 (IL-6) family of cytokines play an important role in initiating and integrating homeostatic responses within the heart. However, these "stress-activated" cytokines all have the potential to produce cardiac decompensation when expressed at sufficiently high concentrations. Indeed, there is now a growing appreciation that these molecules may play an important role in mediating disease progression in the failing heart. The growing appreciation of the pathophysiological consequences of sustained expression of proinflammatory mediators in pre-clinical and clinical heart failure models culminated in a series of multicenter clinical trials that utilized "targeted" approaches to neutralize tumor necrosis factor (TNF) in patients with moderate to advanced heart failure. However, these targeted approaches have resulted in worsening heart failure, thereby raising a number of important questions about what role, if any, proinflammatory cytokines play in the pathogenesis of heart failure. This review will summarize the tremendous growth of knowledge that has taken place in this field, with a focus on what we have learned from the negative clinical trials, as well as the potential direction of future research in this area.     

Discovering local patterns of co - evolution: computational aspects and biological examples

Background

Co-evolution is the process in which two (or more) sets of orthologs exhibit a similar or correlative pattern of evolution. Co-evolution is a powerful way to learn about the functional interdependencies between sets of genes and cellular functions and to predict physical interactions. More generally, it can be used for answering fundamental questions about the evolution of biological systems. Orthologs that exhibit a strong signal of co-evolution in a certain part of the evolutionary tree may show a mild signal of co-evolution in other branches of the tree. The major reasons for this phenomenon are noise in the biological input, genes that gain or lose functions, and the fact that some measures of co-evolution relate to rare events such as positive selection. Previous publications in the field dealt with the problem of finding sets of genes that co-evolved along an entire underlying phylogenetic tree, without considering the fact that often co-evolution is local.

Results

In this work, we describe a new set of biological problems that are related to finding patterns of local co-evolution. We discuss their computational complexity and design algorithms for solving them. These algorithms outperform other bi-clustering methods as they are designed specifically for solving the set of problems mentioned above. We use our approach to trace the co-evolution of fungal, eukaryotic, and mammalian genes at high resolution across the different parts of the corresponding phylogenetic trees. Specifically, we discover regions in the fungi tree that are enriched with positive evolution. We show that metabolic genes exhibit a remarkable level of co-evolution and different patterns of co-evolution in various biological datasets. In addition, we find that protein complexes that are related to gene expression exhibit non-homogenous levels of co-evolution across different parts of the fungi evolutionary line. In the case of mammalian evolution, signaling pathways that are related to neurotransmission exhibit a relatively higher level of co-evolution along the primate subtree.

Conclusions

We show that finding local patterns of co-evolution is a computationally challenging task and we offer novel algorithms that allow us to solve this problem, thus opening a new approach for analyzing the evolution of biological systems.     

Cardiac assist with a twist: apical torsion as a means to improve failing heart function

Changes in muscle fiber orientation across the wall of the left ventricle (LV) cause the apex of the heart to turn 10-15 deg in opposition to its base during systole and are believed to increase stroke volume and lower wall stress in healthy hearts. Studies show that cardiac torsion is sensitive to various disease states, which suggests that it may be an important aspect of cardiac function. Modern imaging techniques have sparked renewed interest in cardiac torsion dynamics, but no work has been done to determine whether mechanically augmented apical torsion can be used to restore function to failing hearts. In this report, we discuss the potential advantages of this approach and present evidence that turning the cardiac apex by mechanical means can displace a clinically significant volume of blood from failing hearts. Computational models of normal and reduced-function LVs were created to predict the effects of applied apical torsion on ventricular stroke work and wall stress. These same conditions were reproduced in anesthetized pigs with drug-induced heart failure using a custom apical torsion device programmed to rotate over various angles during cardiac systole. Simulations of applied 90 deg torsion in a prolate spheroidal computational model of a reduced-function pig heart produced significant increases in stroke work (25%) and stroke volume with reduced fiber stress in the epicardial region. These calculations were in substantial agreement with corresponding in vivo measurements. Specifically, the computer model predicted torsion-induced stroke volume increases from 13.1 to 14.4 mL (9.9%) while actual stroke volume in a pig heart of similar size and degree of dysfunction increased from 11.1 to 13.0 mL (17.1%). Likewise, peak LV pressures in the computer model rose from 85 to 95 mm Hg (11.7%) with torsion while maximum ventricular pressures in vivo increased in similar proportion, from 55 to 61 mm Hg (10.9%). These data suggest that: (a) the computer model of apical torsion developed for this work is a fair and accurate predictor of experimental outcomes, and (b) supra-physiologic apical torsion may be a viable means to boost cardiac output while avoiding blood contact that occurs with other assist methods.     

Relative contributions of local cell and passing fiber activation and silencing to changes in thalamic fidelity during deep brain stimulation and lesioning: a computational modeling study

Deep brain stimulation (DBS) and lesioning are two surgical techniques used in the treatment of advanced Parkinson’s disease (PD) in patients whose symptoms are not well controlled by drugs, or who experience dyskinesias as a side effect of medications. Although these treatments have been widely practiced, the mechanisms behind DBS and lesioning are still not well understood. The subthalamic nucleus (STN) and globus pallidus pars interna (GPi) are two common targets for both DBS and lesioning. Previous studies have indicated that DBS not only affects local cells within the target, but also passing axons within neighboring regions. Using a computational model of the basal ganglia-thalamic network, we studied the relative contributions of activation and silencing of local cells (LCs) and fibers of passage (FOPs) to changes in the accuracy of information transmission through the thalamus (thalamic fidelity), which is correlated with the effectiveness of DBS. Activation of both LCs and FOPs during STN and GPi-DBS were beneficial to the outcome of stimulation. During STN and GPi lesioning, effects of silencing LCs and FOPs were different between the two types of lesioning. For STN lesioning, silencing GPi FOPs mainly contributed to its effectiveness, while silencing only STN LCs did not improve thalamic fidelity. In contrast, silencing both GPi LCs and GPe FOPs during GPi lesioning contributed to improvements in thalamic fidelity. Thus, two distinct mechanisms produced comparable improvements in thalamic function: driving the output of the basal ganglia to produce tonic inhibition and silencing the output of the basal ganglia to produce tonic disinhibition. These results show the importance of considering effects of activating or silencing fibers passing close to the nucleus when deciding upon a target location for DBS or lesioning.     

A case study: the effect of visitors on two captive pumas with respect to the time of the day

This study analyzed the effects of noise levels and number of visitors on the behaviors of a mother puma and her daughter in a zoo environment with respect to the time of day. The study monitored visitation (noise and number) over two 1-week periods (4 weeks between periods) and frequency of various puma behaviors (videorecorded). The study analyzed videotaped behavior of the pumas based on the time of day and visitors' number and noise levels. There was a direct association of puma behaviors with visitors' number and noise levels. The daughter puma was the most affected and behavioral changes of both pumas correlated more strongly with the noise level than the number of visitors. The noise level and number of visitors affected the behavior of the mother and her daughter only in the morning. The results of this study indicate that both noise level and number of visitors affected these pumas but revealed the noise as predominant. Moreover, the response of these pumas to visitors depended on the time of the day.     

Simultaneous response of myocardial contractility and a major proteolytic process to beta-adrenergic-receptor occupancy in the Langendorff isolated perfused rat heart.

The Langendorff isolated rat heart was adapted to the study of minute-to-minute percentage changes in bulk protein degradation by using non-recirculating perfusion. Hearts were perfused at 8 ml/min at 35 degrees C with Krebs-Henseleit buffer containing 11 mM-glucose, and only hearts with regular ventricular rhythm were employed. Proteins were labelled by infusion of [3H]leucine for 0.5 h in vitro. A complete amino acid mixture was then added at 3 times normal rat extracellular concentrations. After labelling, the re-incorporation of [3H]leucine was competitively inhibited by addition of either 4 mM-leucine or 20 microM-cycloheximide. The residual unincorporated radioactivity and the preferentially labelled rapid-turnover proteins were eliminated during a 3 h preliminary perfusion period. The basal rate of release of [3H]leucine and percentage changes were then determined at 1 min intervals, by using each heart as its own control. Leucine metabolism was inconsequential to results. Exchange of intracellular leucine pools with extracellular leucine and subsequent release in effluent perfusate was 95% complete within approx. 2 min. The basal rate of protein degradation was unchanged by electrical stimulation of the heart rate to 360 beats/min or cessation of contractile activity by membrane depolarization under 25 mM-KCl. Infusion of the beta-agonist isoprenaline at 5-500 nM caused a graded inhibition of myocardial protein degradation within 5-6 min, with a maximum inhibition of 30%. This inhibition was sustained for at least 1 h of drug administration and was reversed within 4-6 min of cessation of isoprenaline or simultaneous infusion of 1 microM of the beta-receptor antagonist propranolol. Minute-to-minute adrenergic proteolytic control was a simultaneous co-variable with beta-receptor-mediated inotropic changes in right-intraventricular systolic pressure. Stoppage of the heart in asystole by the Ca2+-channel blocker nifedipine (0.7 microM) delayed the onset, but did not cause sustained reversal, of adrenergic-inhibited degradation, indicating the absence of a direct obligatory mechanistic linkage between the events of the contraction-relaxation cycle and protein degradation in this preparation.     

The study of a strain ofCandida utilis in the course of continuous cultivation on ethanol with special respect to biotin requirement

It was found using a long-term continuous cultivation in a synthetic ethanol medium that a strain ofCandida utilis can permanently form a sufficient amount of growth factors. This fact is confirmed both by high yields of biomass and steady level of biotin in the yeast mass. Composition of proteins is the same as in yeasts grown on other carbon sources.     

B cell activation triggered by the formation of the small receptor cluster: a computational study

We proposed a spatially extended model of early events of B cell receptors (BCR) activation, which is based on mutual kinase-receptor interactions that are characteristic for the immune receptors and the Src family kinases. These interactions lead to the positive feedback which, together with two nonlinearities resulting from the double phosphorylation of receptors and Michaelis-Menten dephosphorylation kinetics, are responsible for the system bistability. We demonstrated that B cell can be activated by a formation of a tiny cluster of receptors or displacement of the nucleus. The receptors and Src kinases are activated, first locally, in the locus of the receptor cluster or the region where the cytoplasm is the thinnest. Then the traveling wave of activation propagates until activity spreads over the whole cell membrane. In the models in which we assume that the kinases are free to diffuse in the cytoplasm, we found that the fraction of aggregated receptors, capable to initiate B cell activation decreases with the decreasing thickness of cytoplasm and decreasing kinase diffusion. When kinases are restricted to the cell membrane - which is the case for most of the Src family kinases - even a cluster consisting of a tiny fraction of total receptors becomes activatory. Interestingly, the system remains insensitive to the modest changes of total receptor level. The model provides a plausible mechanism of B cells activation due to the formation of small receptors clusters collocalized by binding of polyvalent antigens or arising during the immune synapse formation.     

Minimal oxygen consumption and optimal contractility of the heart: Theoretical approach to principle of physiological control of contractility

Oxygen consumption of the left ventricle (MVO ₂) was evaluated theoretically under the condition that the ventricle pumps a constant stroke volume against a constant arterial pressure, hence producing a constant external mechanical stroke work, with a widely varied contractility.MVO ₂ was calculated by an empirical equation which had been inferred previously. Theoretical results indicated that the ventricle has a contractility at whichMVO ₂ is minimal in spite of constant external work and therefore the mechanical efficiency as a pump is maximal. Such a contractility can be considered to be optimal from a standpoint of metabolic economy. The optimal contractility fell within the physiological range of contractility which had been observed experimentally. The result suggests a possibility that the contractility of a normal heart might be physiologically adapted to such an optimal level.     

Biogeographical contrasts to assess local and regional patterns of invasion: a case study with two reciprocally introduced exotic maple trees

Quantitative comparisons of distribution and abundance of exotic species in their native and non‐native ranges represent a first step when studying invaders. However, this approach is rarely applied 2 particularly to tree species. Using biogeographical contrasts coupled with regional dispersal surveys, we assessed whether two exotic maple tree species, Acer negundo and Acer platanoides, can be classified as invasive in the non‐native regions surveyed. We also examined the importance of biogeography in determining the degree of invasion by exotic species using this reciprocal approach. Local‐scale surveys were conducted in a total of 34 forests to compare density, relative abundance, age structure of native and introduced populations, and whether the two introduced maple species negatively affected native tree species density. Regional‐scale surveys of a total of 136 forests were then conducted to assess distribution in the introduced regions. Introduced populations of A. negundo were denser than populations measured in their native range and negatively related to native tree species density. Age structure did not differ between regions for this species. At the regional scale, this species has invaded most of the riparian corridors sampled in France. Conversely, the density of A. platanoides introduced populations was similar to that of native populations and was not related to native tree species density. Although seedling recruitment was higher away than at home, this species has invaded only 9% of the forests sampled in southern Ontario, Canada. Although reported invasive, these two exotic maple species differed in their relative demographic parameters and regional spread. Acer negundo is currently invasive in southern France while A. platanoides is not aggressively invasive in southern Ontario. Importantly, this study effectively demonstrates that biogeography through structured contrasts provide a direct means to infer invasion of exotic species.     

Computer analysis of ventricular pressure recordings: evaluation of myocardial contractility on the dog heart in situ]

The contractile indices Vmax (maximum shortening velocity of the contractile element) and ARPD (power averaged rate of power density generation) which have been shown to be unaffected by alterations in preload and afterload were computed from isovolumic left ventricular pressure data of dogs. The two indices were tested for their ability to detect changes in contractility induced by a positive inotropic drug (Isoprenalin). Whereas a good correlation was found between ARPD and Vmax (coefficient of correlation 0,895) the index ARPD was more sensitive to augmentation of myocardial contractility; also because it is simpler to obtain computationally and more appropriate for the intact heart from a theoretical point of view. ARPD should be useful especially for quantification of acute changes in myocardial contractility.     

Interaction of glucosamine with uracil and thymine: a computational study

Noncovalent interactions are ubiquitous and have been well recognized in chemistry, biology and material science. Yet, there are still recurring controversies over their natures, due to the wide range of noncovalent interaction terms. In this Essay, we employed the Valence Bond (VB) methods to address two types of interactions which recently have drawn intensive attention, i.e., the halogen bonding and the CH???HC dihydrogen bonding. The VB methods have the advantage of interpreting molecular structures and properties in the term of electron-localized Lewis (resonance) states (structures), which thereby shed specific light on the alteration of the bonding patterns. Due to the electron localization nature of Lewis states, it is possible to define individually and measure both polarization and charge transfer effects which have different physical origins. We demonstrated that both the ab initio VB method and the block-localized wavefunction (BLW) method can provide consistent pictures for halogen bonding systems, where strong Lewis bases NH₃, H₂O and NMe₃ partake as the halogen bond acceptors, and the halogen bond donors include dihalogen molecules and XNO₂ (X?=?Cl, Br, I). Based on the structural, spectral, and energetic changes, we confirm the remarkable roles of charge transfer in these halogen bonding complexes. Although the weak C-H???H-C interactions in alkane dimers and graphane sheets are thought to involve dispersion only, we show that this term embeds delicate yet important charge transfer, bond reorganization and polarization interactions.

     

The atrial myocardial cells of mouse heart: a structural and stereological study

Structural and stereological studies of mouse atrial myocardial cells, carried out in the same fashion as our previous investigations on mouse ventricle, demonstrate an extremely well-developed sarcoplasmic reticulum (SR) in atrial cells. The volume fraction (Vv) of the SR exceeds 12% in mouse atrial cells; perimyofibrillar network SR constitutes the major portion. We have confirmed the findings of Bossen et al. (1981, Tissue Cell 13, 71-77) of a difference between atria in terms of coupling density, the right atrium having a significantly lower incidence of interior junctional SR than the left. The SR of mouse atrium comprises a rich variety of specialized segments, including the IJSR, peripheral junctional SR, corbular SR, cisternal SR (including regions similar to fenestrated collars of striated skeletal muscle SR), as well as a peculiar form of extended junctional SR (EJSR). Although less frequent in occurrence than corbular SR, the EJSR seems closely related, since it occurs in multiple clusters at or near the Z-line regions, contains internal granular densities, and bears surface-connected structures resembling junctional processes. Seen in thin sections, mouse atrial EJSR elements are more complex than corbular SR, being larger in diameter and frequently circular in profile. Thick-section and serial-section analyses reveal that bodies of EJSR are in fact hollow spheroids. The transverse-axial tubular system of mouse atrium is rather poorly developed in comparison to its ventricular counterpart. The Golgi apparatus and associated specific atrial granules are prominent cell components. "Focal ellipsoidal deposits" (FEDs) previously described by Page and co-workers (1986, Amer. J. Physiol.) are consistently located adjacent to the Golgi region, but immunocytochemical staining for two different segments of atrial natriuretic peptide reveals no specific reaction in FEDs, whereas the SAGs are densely labeled for both antibodies.